bot_bottle/agent_provider.py

@@ -240,7 +240,7 @@ class AgentProvider(ABC):
         BottleBackend.provision_workspace against the running bottle."""
         from .log import info
 
-        manifest_bottle = plan.spec.manifest.bottle_for(plan.spec.agent_name)
+        manifest_bottle = plan.manifest.bottle
         if manifest_bottle.git:
             from .git_gate import GIT_GATE_HOSTNAME, git_gate_render_gitconfig
             gate_host = getattr(plan, "git_gate_insteadof_host", GIT_GATE_HOSTNAME)

bot_bottle/backend/__init__.py

@@ -45,7 +45,7 @@ from ..agent_provider import AgentProvisionPlan, get_provider, build_agent_provi
 from ..egress import EgressPlan
 from ..git_gate import GitGatePlan
 from ..log import die, info
-from ..manifest import Manifest
+from ..manifest import Manifest, ManifestIndex
 from ..supervise import SupervisePlan
 from ..util import expand_tilde
 from ..env import resolve_env, ResolvedEnv
@@ -61,7 +61,7 @@ class BottleSpec:
     Resolved values (image names, container name, scratch paths, runsc
     availability) live on the plan, not the spec."""
 
-    manifest: Manifest
+    manifest: ManifestIndex
     agent_name: str
     copy_cwd: bool
     user_cwd: str
@@ -80,6 +80,7 @@ class BottlePlan(ABC):
     (e.g. DockerBottlePlan) add backend-specific resolved fields."""
 
     spec: BottleSpec
+    manifest: Manifest
     stage_dir: Path
     git_gate_plan: GitGatePlan
 
@@ -112,9 +113,9 @@ class BottlePlan(ABC):
         """Render the y/N preflight summary to stderr."""
         del remote_control
         spec = self.spec
-        manifest = spec.manifest
-        agent = manifest.agents[spec.agent_name]
-        bottle = manifest.bottle_for(spec.agent_name)
+        manifest = self.manifest
+        agent = manifest.agent
+        bottle = manifest.bottle
 
         env_names = visible_agent_env_names(
             sorted(
@@ -131,7 +132,7 @@ class BottlePlan(ABC):
         print_multi("skills          ", list(agent.skills))
         info(f"bottle          : {agent.bottle}")
 
-        identity = manifest.git_identity_summary(spec.agent_name)
+        identity = manifest.git_identity_summary()
         if identity:
             info(f"  git identity  : {identity}")
 
@@ -289,15 +290,14 @@ class BottleBackend(ABC, Generic[PlanT, CleanupT]):
             write_launch_metadata,
         )
 
-        self._validate(spec)
+        manifest = self._validate(spec)
 
         self._preflight()
 
-        manifest = spec.manifest
-        manifest_bottle = manifest.bottle_for(spec.agent_name)
+        manifest_bottle = manifest.bottle
         manifest_agent_provider = manifest_bottle.agent_provider
         agent_provider = get_provider(manifest_agent_provider.template)
-        resolved_env = resolve_env(manifest, spec.agent_name)
+        resolved_env = resolve_env(manifest)
         workspace = workspace_plan(spec, guest_home=agent_provider.guest_home)
 
         slug = mint_slug(spec)
@@ -313,7 +313,7 @@ class BottleBackend(ABC, Generic[PlanT, CleanupT]):
         else:
             agent_dockerfile_path = str(agent_provider.dockerfile)
 
-        agent_dir, prompt_file = prepare_agent_state_dir(slug, spec)
+        agent_dir, prompt_file = prepare_agent_state_dir(slug, manifest)
 
         agent_provision_plan = build_agent_provision_plan(
             template=manifest_agent_provider.template,
@@ -337,6 +337,7 @@ class BottleBackend(ABC, Generic[PlanT, CleanupT]):
 
         return self._resolve_plan(
             spec,
+            manifest=manifest,
             slug=slug,
             resolved_env=resolved_env,
             agent_provision_plan=agent_provision_plan,
@@ -355,16 +356,18 @@ class BottleBackend(ABC, Generic[PlanT, CleanupT]):
         """
         pass
 
-    def _validate(self, spec: BottleSpec) -> None:
-        """Cross-backend pre-launch checks. Confirms the agent exists
-        and the named skills are present on the host. Subclasses with
+    def _validate(self, spec: BottleSpec) -> Manifest:
+        """Cross-backend pre-launch checks. Parses the selected agent and
+        its bottle (raising ManifestError on invalid content), confirms
+        skills are present on the host, and every git IdentityFile resolves.
+
+        Returns the loaded Manifest for the selected agent. Subclasses with
         additional preconditions should override and call
         `super()._validate(spec)` first."""
-        manifest = spec.manifest
-        manifest.require_agent(spec.agent_name)
-        agent = manifest.agents[spec.agent_name]
-        self._validate_skills(agent.skills)
-        self._validate_agent_provider_dockerfile(spec)
+        manifest = spec.manifest.load_for_agent(spec.agent_name)
+        self._validate_skills(manifest.agent.skills)
+        self._validate_agent_provider_dockerfile(spec, manifest)
+        return manifest
 
     def _validate_skills(self, skills: Sequence[str]) -> None:
         """Each named skill must be a directory under the host's
@@ -378,8 +381,8 @@ class BottleBackend(ABC, Generic[PlanT, CleanupT]):
                     f"Create it under ~/.claude/skills/, then re-run."
                 )
 
-    def _validate_agent_provider_dockerfile(self, spec: BottleSpec) -> None:
-        bottle = spec.manifest.bottle_for(spec.agent_name)
+    def _validate_agent_provider_dockerfile(self, spec: BottleSpec, manifest: Manifest) -> None:
+        bottle = manifest.bottle
         dockerfile = bottle.agent_provider.dockerfile
         if not dockerfile:
             return
@@ -389,13 +392,14 @@ class BottleBackend(ABC, Generic[PlanT, CleanupT]):
         if not path.is_file():
             die(
                 f"agent_provider.dockerfile for bottle "
-                f"'{spec.manifest.agents[spec.agent_name].bottle}' not found: {path}"
+                f"'{manifest.agent.bottle}' not found: {path}"
             )
 
     @abstractmethod
     def _resolve_plan(self,
                       spec: BottleSpec,
                       *,
+                      manifest: Manifest,
                       slug: str,
                       resolved_env: ResolvedEnv,
                       agent_provision_plan: AgentProvisionPlan,

bot_bottle/backend/docker/backend.py

@@ -30,6 +30,7 @@ from ...egress import EgressPlan
 from ...env import ResolvedEnv
 from ...git_gate import GitGatePlan
 from ...supervise import SupervisePlan
+from ...manifest import Manifest
 from .. import ActiveAgent, BottleBackend, BottleSpec
 from . import cleanup as _cleanup
 from . import enumerate as _enumerate
@@ -63,6 +64,7 @@ class DockerBottleBackend(BottleBackend["DockerBottlePlan", "DockerBottleCleanup
         self,
         spec: BottleSpec,
         *,
+        manifest: Manifest,
         slug: str,
         resolved_env: ResolvedEnv,
         agent_provision_plan: AgentProvisionPlan,
@@ -73,6 +75,7 @@ class DockerBottleBackend(BottleBackend["DockerBottlePlan", "DockerBottleCleanup
     ) -> DockerBottlePlan:
         return _resolve_plan.resolve_plan(
             spec,
+            manifest=manifest,
             slug=slug,
             resolved_env=resolved_env,
             agent_provision_plan=agent_provision_plan,

bot_bottle/backend/docker/launch.py

@@ -75,7 +75,7 @@ def launch(
     Teardown on exit."""
     stack = ExitStack()
 
-    _bottle_for_revoke = plan.spec.manifest.bottle_for(plan.spec.agent_name)
+    _bottle_for_revoke = plan.manifest.bottle
     _git_gate_dir_for_revoke = git_gate_state_dir(plan.slug)
 
     def teardown() -> None:

bot_bottle/backend/docker/resolve_plan.py

@@ -18,6 +18,7 @@ from .. import BottleSpec
 from ...env import ResolvedEnv
 from ...agent_provider import AgentProvisionPlan
 from ...egress import EgressPlan
+from ...manifest import Manifest
 from ...supervise import SupervisePlan
 from ...git_gate import GitGatePlan
 
@@ -31,6 +32,7 @@ def build_guest_env(resolved_env: ResolvedEnv) -> dict[str, str]:
 
 def resolve_plan(
     spec: BottleSpec,
+    manifest: Manifest,
     slug: str,
     resolved_env: ResolvedEnv,
     agent_provision_plan: AgentProvisionPlan,
@@ -48,6 +50,7 @@ def resolve_plan(
 
     return DockerBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=stage_dir,
         slug=slug,
         forwarded_env=dict(resolved_env.forwarded),

bot_bottle/backend/macos_container/backend.py

@@ -11,6 +11,7 @@ from ...egress import EgressPlan
 from ...env import ResolvedEnv
 from ...git_gate import GitGatePlan
 from ...supervise import SupervisePlan
+from ...manifest import Manifest
 from .. import ActiveAgent, BottleBackend, BottleSpec
 from . import cleanup as _cleanup
 from . import enumerate as _enumerate
@@ -45,6 +46,7 @@ class MacosContainerBottleBackend(
         self,
         spec: BottleSpec,
         *,
+        manifest: Manifest,
         slug: str,
         resolved_env: ResolvedEnv,
         agent_provision_plan: AgentProvisionPlan,
@@ -55,6 +57,7 @@ class MacosContainerBottleBackend(
     ) -> MacosContainerBottlePlan:
         return _resolve_plan.resolve_plan(
             spec,
+            manifest=manifest,
             slug=slug,
             resolved_env=resolved_env,
             agent_provision_plan=agent_provision_plan,

bot_bottle/backend/macos_container/launch.py

@@ -68,7 +68,7 @@ def launch(
 ) -> Generator[MacosContainerBottle, None, None]:
     """Build, run, provision, and yield an Apple Container bottle."""
     stack = ExitStack()
-    bottle_for_revoke = plan.spec.manifest.bottle_for(plan.spec.agent_name)
+    bottle_for_revoke = plan.manifest.bottle
     git_gate_dir_for_revoke = git_gate_state_dir(plan.slug)
 
     def teardown() -> None:

bot_bottle/backend/macos_container/resolve_plan.py

@@ -9,6 +9,7 @@ from ...egress import EgressPlan
 from ...env import ResolvedEnv
 from ...git_gate import GitGatePlan
 from ...supervise import SupervisePlan
+from ...manifest import Manifest
 from .. import BottleSpec
 from . import util as container_mod
 from .bottle_plan import MacosContainerBottlePlan
@@ -24,6 +25,7 @@ def build_guest_env(resolved_env: ResolvedEnv) -> dict[str, str]:
 
 def resolve_plan(
     spec: BottleSpec,
+    manifest: Manifest,
     slug: str,
     resolved_env: ResolvedEnv,
     agent_provision_plan: AgentProvisionPlan,
@@ -34,6 +36,7 @@ def resolve_plan(
 ) -> MacosContainerBottlePlan:
     return MacosContainerBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=stage_dir,
         slug=slug,
         forwarded_env=dict(resolved_env.forwarded),

bot_bottle/backend/resolve_common.py

@@ -26,7 +26,7 @@ from ..bottle_state import (
 )
 from ..egress import Egress, EgressPlan
 from ..git_gate import GitGate, GitGatePlan
-from ..manifest import ManifestBottle
+from ..manifest import Manifest, ManifestBottle
 from ..supervise import Supervise, SupervisePlan
 from . import BottleSpec
 
@@ -66,11 +66,10 @@ def write_launch_metadata(
     ))
 
 
-def prepare_agent_state_dir(slug: str, spec: BottleSpec) -> tuple[Path, Path]:
+def prepare_agent_state_dir(slug: str, manifest: Manifest) -> tuple[Path, Path]:
     """Create the agent state subdir, write the prompt file.
     Returns (agent_dir, prompt_file)."""
-    manifest = spec.manifest
-    agent = manifest.agents[spec.agent_name]
+    agent = manifest.agent
     agent_dir = agent_state_dir(slug)
     agent_dir.mkdir(parents=True, exist_ok=True)
     prompt_file = agent_dir / "prompt.txt"

bot_bottle/backend/smolmachines/backend.py

@@ -18,6 +18,7 @@ from ...egress import EgressPlan
 from ...env import ResolvedEnv
 from ...git_gate import GitGatePlan
 from ...supervise import SupervisePlan
+from ...manifest import Manifest
 from .. import ActiveAgent, BottleBackend, BottleSpec
 from . import cleanup as _cleanup
 from . import enumerate as _enumerate
@@ -55,6 +56,7 @@ class SmolmachinesBottleBackend(
         self,
         spec: BottleSpec,
         *,
+        manifest: Manifest,
         slug: str,
         resolved_env: ResolvedEnv,
         agent_provision_plan: AgentProvisionPlan,
@@ -65,6 +67,7 @@ class SmolmachinesBottleBackend(
     ) -> SmolmachinesBottlePlan:
         return _resolve_plan.resolve_plan(
             spec,
+            manifest=manifest,
             slug=slug,
             resolved_env=resolved_env,
             agent_provision_plan=agent_provision_plan,

bot_bottle/backend/smolmachines/launch.py

@@ -130,7 +130,7 @@ def _teardown_smolmachines(
     except BaseException as exc:  # noqa: W0718 — teardown must not fail
         teardown_exc = exc
         warn(f"smolmachines teardown failed: {exc!r}")
-    bottle = plan.spec.manifest.bottle_for(plan.spec.agent_name)
+    bottle = plan.manifest.bottle
     revoke_git_gate_provisioned_keys(bottle, git_gate_state_dir(plan.slug))
     if teardown_exc is not None:
         raise teardown_exc

bot_bottle/backend/smolmachines/resolve_plan.py

@@ -13,6 +13,7 @@ from __future__ import annotations
 from pathlib import Path
 
 from .. import BottleSpec
+from ...manifest import Manifest
 from ...env import ResolvedEnv
 from ...agent_provider import AgentProvisionPlan
 from ...egress import EgressPlan
@@ -46,6 +47,7 @@ def build_guest_env(resolved_env: ResolvedEnv) -> dict[str, str]:
 
 def resolve_plan(
     spec: BottleSpec,
+    manifest: Manifest,
     slug: str,
     resolved_env: ResolvedEnv,
     agent_provision_plan: AgentProvisionPlan,
@@ -67,6 +69,7 @@ def resolve_plan(
 
     return SmolmachinesBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=stage_dir,
         slug=slug,
         bundle_subnet=subnet,

bot_bottle/cli/info.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 import argparse
 
 from ..log import info
-from ..manifest import Manifest
+from ..manifest import ManifestIndex
 from ._common import PROG, USER_CWD
 
 
@@ -14,11 +14,12 @@ def cmd_info(argv: list[str]) -> int:
     parser.add_argument("name", help="agent name defined in bot-bottle.json")
     args = parser.parse_args(argv)
 
-    manifest = Manifest.resolve(USER_CWD)
-    manifest.require_agent(args.name)
+    names = ManifestIndex.resolve(USER_CWD)
+    names.require_agent(args.name)
+    manifest = names.load_for_agent(args.name)
 
-    agent = manifest.agents[args.name]
-    bottle = manifest.bottle_for(args.name)
+    agent = manifest.agent
+    bottle = manifest.bottle
     env_names = list(bottle.env.keys())
     prompt_first_line = agent.prompt.splitlines()[0] if agent.prompt else ""
 
@@ -31,7 +32,7 @@ def cmd_info(argv: list[str]) -> int:
         f"first line: {prompt_first_line or '(empty)'}"
     )
     info(f"bottle             : {agent.bottle}")
-    identity = manifest.git_identity_summary(args.name)
+    identity = manifest.git_identity_summary()
     if identity:
         info(f"  git identity  : {identity}")
     if bottle.git:

bot_bottle/cli/list.py

@@ -7,7 +7,7 @@ import os
 import sys
 
 from ..backend import enumerate_active_agents
-from ..manifest import Manifest
+from ..manifest import ManifestIndex
 from ._common import PROG, USER_CWD
 
 _ANSI_COLOR_CODES: dict[str, str] = {
@@ -40,8 +40,8 @@ def cmd_list(argv: list[str]) -> int:
     args = parser.parse_args(argv)
 
     if args.scope == "available":
-        manifest = Manifest.resolve(USER_CWD)
-        for name in manifest.agents.keys():
+        manifest = ManifestIndex.resolve(USER_CWD)
+        for name in manifest.all_agent_names:
             print(name)
         return 0
 

bot_bottle/cli/resume.py

@@ -20,7 +20,7 @@ import argparse
 from ..backend import BottleSpec
 from ..bottle_state import read_metadata
 from ..log import die
-from ..manifest import Manifest
+from ..manifest import ManifestIndex
 from ._common import PROG, USER_CWD
 from .start import _launch_bottle
 
@@ -42,7 +42,7 @@ def cmd_resume(argv: list[str]) -> int:
             f"check ~/.bot-bottle/state/ or run `cli.py start` to create a new bottle"
         )
 
-    manifest = Manifest.resolve(USER_CWD)
+    manifest = ManifestIndex.resolve(USER_CWD)
     manifest.require_agent(metadata.agent_name)
 
     spec = BottleSpec(

bot_bottle/cli/start.py

@@ -33,7 +33,7 @@ from ..bottle_state import (
 )
 # from ..backend.docker.capability_apply import snapshot_transcript
 from ..log import info
-from ..manifest import Manifest
+from ..manifest import ManifestIndex
 from ._common import PROG, USER_CWD, read_tty_line
 from . import tui
 
@@ -62,12 +62,12 @@ def cmd_start(argv: list[str]) -> int:
 
     dry_run = args.dry_run or os.environ.get("BOT_BOTTLE_DRY_RUN") == "1"
 
-    manifest = Manifest.resolve(USER_CWD)
+    manifest = ManifestIndex.resolve(USER_CWD)
 
     agent_name: str | None = args.name
     if agent_name is None:
         agent_name = tui.filter_select(
-            sorted(manifest.agents.keys()),
+            manifest.all_agent_names,
             title="Select agent",
         )
         if agent_name is None:

bot_bottle/contrib/claude/agent_provider.py

@@ -211,7 +211,7 @@ class ClaudeAgentProvider(AgentProvider):
         when the agent has no skills."""
         from ...backend.util import host_skill_dir
 
-        agent = plan.spec.manifest.agents[plan.spec.agent_name]
+        agent = plan.manifest.agent
         if not agent.skills:
             return
         skills_dir = _skills_dir(plan.guest_home)
@@ -240,7 +240,7 @@ class ClaudeAgentProvider(AgentProvider):
             f"chown node:node {prompt_path} && chmod 600 {prompt_path}",
             user="root",
         )
-        agent = plan.spec.manifest.agents[plan.spec.agent_name]
+        agent = plan.manifest.agent
         return prompt_path if plan.agent_provision.has_prompt or agent.prompt else None
 
     def provision(self, plan: "BottlePlan", bottle: "Bottle") -> None:

bot_bottle/contrib/codex/agent_provider.py

@@ -177,7 +177,7 @@ class CodexAgentProvider(AgentProvider):
         skills."""
         from ...backend.util import host_skill_dir
 
-        agent = plan.spec.manifest.agents[plan.spec.agent_name]
+        agent = plan.manifest.agent
         if not agent.skills:
             return
         skills_dir = _skills_dir(plan.guest_home)
@@ -206,7 +206,7 @@ class CodexAgentProvider(AgentProvider):
             f"chown node:node {prompt_path} && chmod 600 {prompt_path}",
             user="root",
         )
-        agent = plan.spec.manifest.agents[plan.spec.agent_name]
+        agent = plan.manifest.agent
         return prompt_path if plan.agent_provision.has_prompt or agent.prompt else None
 
     def provision(self, plan: "BottlePlan", bottle: "Bottle") -> None:

bot_bottle/contrib/pi/agent_provider.py

@@ -232,7 +232,7 @@ class PiAgentProvider(AgentProvider):
     def provision_skills(self, plan: "BottlePlan", bottle: "Bottle") -> None:
         from ...backend.util import host_skill_dir
 
-        agent = plan.spec.manifest.agents[plan.spec.agent_name]
+        agent = plan.manifest.agent
         if not agent.skills:
             return
         skills_dir = _skills_dir(plan.guest_home)

bot_bottle/env.py

@@ -114,7 +114,7 @@ def _read_secret_silent(name: str, prompt_body: str) -> str:
     return value
 
 
-def resolve_env(manifest: Manifest, agent: str) -> ResolvedEnv:
+def resolve_env(manifest: Manifest) -> ResolvedEnv:
     """Iterate the agent's env entries:
       - secret:       prompt at runtime; carry value in forwarded
       - interpolated: read $HOST_VAR from os.environ; carry value in forwarded
@@ -124,7 +124,7 @@ def resolve_env(manifest: Manifest, agent: str) -> ResolvedEnv:
     backend injects forwarded values via its launcher's env parameter."""
     forwarded: dict[str, str] = {}
     literals: dict[str, str] = {}
-    bottle = manifest.bottle_for(agent)
+    bottle = manifest.bottle
     for name, raw in bottle.env.items():
         if not name:
             continue

bot_bottle/manifest.py

@@ -36,10 +36,23 @@ Bottles can ONLY live under $HOME. A bottles/ dir under $CWD is a
 warn at load time and contributes nothing. The trust boundary is
 expressed as filesystem layout rather than resolver logic.
 
-Validation runs once at load. Manifest.from_json_obj is preserved
-as a programmatic entry point (used by tests) that takes a dict
-with the same field names — useful for building manifests without
-on-disk files.
+Two types are exported:
+
+  ManifestIndex  — the multi-agent/bottle collection returned by
+                   resolve() and from_json_obj(). Used for agent
+                   selection (all_agent_names), validation
+                   (require_agent), and lazy loading (load_for_agent).
+                   This is the pre-preflight form.
+
+  Manifest       — a single-agent/bottle value type holding exactly
+                   one agent: ManifestAgent and one bottle:
+                   ManifestBottle (with the agent's git-gate.user
+                   already overlaid). Returned by load_for_agent().
+                   This is the post-preflight form passed to backends.
+
+ManifestIndex.from_json_obj is preserved as a programmatic entry
+point (used by tests) that takes a dict with the same field names —
+useful for building manifests without on-disk files.
 """
 
 from __future__ import annotations
@@ -71,6 +84,7 @@ __all__ = [
     "ManifestEgressConfig",
     "ManifestAgent",
     "ManifestBottle",
+    "ManifestIndex",
     "Manifest",
 ]
 
@@ -189,14 +203,64 @@ class ManifestBottle:
         )
 
 
+def _merge_git_user(
+    agent_user: ManifestGitUser, base_user: ManifestGitUser
+) -> ManifestGitUser:
+    """Merge the agent's git.user over the bottle's, agent-wins-on-non-empty."""
+    if agent_user.is_empty():
+        return base_user
+    return ManifestGitUser(
+        name=agent_user.name or base_user.name,
+        email=agent_user.email or base_user.email,
+    )
+
+
 @dataclass(frozen=True)
 class Manifest:
+    """Single-agent/bottle value type. Returned by ManifestIndex.load_for_agent().
+
+    `bottle` is the effective bottle with the agent's git-gate.user already
+    overlaid per-field (agent wins on non-empty). Backends and provisioners
+    use this directly — no agent_name lookup needed."""
+
+    agent: ManifestAgent
+    bottle: ManifestBottle
+
+    def git_identity_summary(self) -> str | None:
+        """One-line effective git identity with per-field provenance, e.g.
+        `name=claude (agent), email=eric@dideric.is (bottle)`.
+        Returns None when neither agent nor bottle sets an identity."""
+        over = self.agent.git_user        # agent's declared git_user (pre-merge)
+        merged = self.bottle.git_user     # effective git_user (post-merge)
+        if merged.is_empty():
+            return None
+        parts: list[str] = []
+        if merged.name:
+            parts.append(f"name={merged.name} ({'agent' if over.name else 'bottle'})")
+        if merged.email:
+            parts.append(f"email={merged.email} ({'agent' if over.email else 'bottle'})")
+        return ", ".join(parts)
+
+
+@dataclass(frozen=True)
+class ManifestIndex:
+    """Multi-agent/bottle collection. The pre-preflight form.
+
+    In lazy mode (from resolve()/from_md_dirs()) only filenames are scanned;
+    no file content is read. In eager mode (from from_json_obj()) all agents
+    and bottles are pre-parsed. Call load_for_agent() to get a single-value
+    Manifest ready for backend use."""
+
     bottles: Mapping[str, ManifestBottle]
     agents: Mapping[str, ManifestAgent]
+    # Set by from_md_dirs; None in from_json_obj (test/programmatic) mode.
+    # Stores the manifest root dirs so load_for_agent can locate files later.
+    home_md: Path | None = field(default=None)
+    cwd_md: Path | None = field(default=None)
 
     @classmethod
-    def resolve(cls, cwd: str, *, missing_ok: bool = False) -> "Manifest":
-        """Walk the per-file manifest tree and build a Manifest.
+    def resolve(cls, cwd: str, *, missing_ok: bool = False) -> "ManifestIndex":
+        """Walk the per-file manifest tree and build a ManifestIndex.
 
         Layout (PRD 0011):
           $HOME/.bot-bottle/bottles/<name>.md  — bottles (home-only)
@@ -209,7 +273,7 @@ class Manifest:
         boundary.
 
         If `missing_ok` is true, a missing `$HOME/.bot-bottle/`
-        returns an empty manifest instead of dying. This is for
+        returns an empty index instead of dying. This is for
         passive UI surfaces like the dashboard, which can still
         monitor already-running agents without launch config.
 
@@ -248,25 +312,16 @@ class Manifest:
         cls,
         home_dir: Path,
         cwd_dir: Path | None,
-    ) -> "Manifest":
-        """Programmatic entry point. Loads bottles from
-        `<home_dir>/bottles/`, home agents from `<home_dir>/agents/`,
-        and (if `cwd_dir` is passed) cwd agents from
-        `<cwd_dir>/agents/`. Cwd agents override home agents on
-        name collision. A `bottles/` subdir under `cwd_dir` is
-        logged as a warning and ignored.
+    ) -> "ManifestIndex":
+        """Return a names-only ManifestIndex. No file content is read; only
+        filenames are scanned for the agent selector.  Full parsing happens
+        later, per-agent, via `load_for_agent`.
 
-        Used by tests to build a Manifest from fixture directories
+        A `bottles/` subdir under `cwd_dir` is logged as a warning and
+        ignored — the filesystem layout IS the trust boundary.
+
+        Used by tests to build a ManifestIndex from fixture directories
         without touching `os.environ`."""
-        bottles_dir = home_dir / "bottles"
-        from .manifest_loader import load_agents_from_dir, load_bottles_from_dir
-
-        bottles = load_bottles_from_dir(bottles_dir)
-
-        bottle_names = set(bottles.keys())
-        agents_dir = home_dir / "agents"
-        agents = load_agents_from_dir(agents_dir, bottle_names, source="$HOME")
-
         if cwd_dir is not None:
             stale_bottles = cwd_dir / "bottles"
             if stale_bottles.is_dir():
@@ -280,17 +335,11 @@ class Manifest:
                         f"live under $HOME/.bot-bottle/bottles/ "
                         f"(PRD 0011). Move them or delete."
                     )
-            cwd_agents_dir = cwd_dir / "agents"
-            cwd_agents = load_agents_from_dir(
-                cwd_agents_dir, bottle_names, source="$CWD"
-            )
-            agents = {**agents, **cwd_agents}
-
-        return cls(bottles=bottles, agents=agents)
+        return cls(bottles={}, agents={}, home_md=home_dir, cwd_md=cwd_dir)
 
     @classmethod
-    def from_json_obj(cls, obj: object) -> "Manifest":
-        """Validate and build a Manifest from a raw JSON-like dict."""
+    def from_json_obj(cls, obj: object) -> "ManifestIndex":
+        """Validate and build a ManifestIndex from a raw JSON-like dict."""
         d = as_json_object(obj, "manifest")
         raw_bottles_obj = _section_dict(d.get("bottles"), "manifest 'bottles'")
         raw_agents = _section_dict(d.get("agents"), "manifest 'agents'")
@@ -311,75 +360,121 @@ class Manifest:
         }
         return cls(bottles=bottles, agents=agents)
 
+    @property
+    def all_agent_names(self) -> list[str]:
+        """Sorted list of all discoverable agent names.
+
+        In names-only mode (from resolve/from_md_dirs) this scans agent
+        filenames without reading their content. In eager mode (from
+        from_json_obj) it returns the pre-parsed agents' names."""
+        if self.home_md is not None:
+            from .manifest_loader import scan_agent_names
+            home_names = set(scan_agent_names(self.home_md / "agents").keys())
+            cwd_names: set[str] = set()
+            if self.cwd_md is not None:
+                cwd_names = set(scan_agent_names(self.cwd_md / "agents").keys())
+            return sorted(home_names | cwd_names)
+        return sorted(self.agents.keys())
+
+    def load_for_agent(self, agent_name: str) -> "Manifest":
+        """Parse the named agent and its bottle; return a single-value Manifest.
+
+        In lazy mode (from resolve/from_md_dirs) the agent file and its
+        bottle chain are read from disk for the first time here.  In eager
+        mode (from_json_obj) the data is already parsed; this just filters
+        down to the requested agent and its bottle.
+
+        The returned Manifest.bottle has the agent's git-gate.user already
+        overlaid (agent wins on non-empty, per-field).
+
+        Always raises ManifestError if the agent is unknown or invalid.
+        Backends call this at preflight inside _validate."""
+        if self.home_md is None:
+            # Eager manifest (from_json_obj): data already parsed; filter to
+            # the one requested agent and its bottle so the returned Manifest
+            # always holds exactly one agent and one bottle regardless of path.
+            if agent_name not in self.agents:
+                available = ", ".join(sorted(self.agents.keys())) or "(none)"
+                raise ManifestError(
+                    f"agent '{agent_name}' not defined. Available: {available}"
+                )
+            agent = self.agents[agent_name]
+            raw_bottle = self.bottles[agent.bottle]
+            merged = _merge_git_user(agent.git_user, raw_bottle.git_user)
+            bottle = raw_bottle if merged == raw_bottle.git_user else replace(raw_bottle, git_user=merged)
+            return Manifest(agent=agent, bottle=bottle)
+
+        from .manifest_loader import load_bottle_chain_from_dir, scan_agent_names
+        from .manifest_schema import validate_agent_frontmatter_keys
+        from .yaml_subset import YamlSubsetError, parse_frontmatter
+
+        # Locate the agent file; cwd wins over home on name collision.
+        home_agents = scan_agent_names(self.home_md / "agents")
+        cwd_agents: dict[str, Path] = {}
+        if self.cwd_md is not None:
+            cwd_agents = scan_agent_names(self.cwd_md / "agents")
+        merged_agents = {**home_agents, **cwd_agents}
+
+        if agent_name not in merged_agents:
+            available = ", ".join(sorted(merged_agents.keys())) or "(none)"
+            raise ManifestError(
+                f"agent '{agent_name}' not defined. Available: {available}"
+            )
+
+        agent_path = merged_agents[agent_name]
+        try:
+            fm, body = parse_frontmatter(agent_path.read_text())
+        except OSError as e:
+            raise ManifestError(f"could not read {agent_path}: {e}") from e
+        except YamlSubsetError as e:
+            raise ManifestError(f"{agent_path}: {e}") from e
+
+        validate_agent_frontmatter_keys(agent_path, fm.keys())
+
+        bottle_name = fm.get("bottle")
+        if not isinstance(bottle_name, str) or not bottle_name:
+            raise ManifestError(
+                f"agent '{agent_name}' must declare a 'bottle' field "
+                f"naming a defined bottle"
+            )
+
+        # Load the bottle chain (may raise ManifestError).
+        bottles_dir = self.home_md / "bottles"
+        raw_bottle = load_bottle_chain_from_dir(bottle_name, bottles_dir)
+
+        # Build and validate the full ManifestAgent.
+        agent_dict: dict[str, object] = {
+            "bottle": bottle_name,
+            "skills": fm.get("skills", []),
+            "prompt": body.strip(),
+        }
+        if "git-gate" in fm:
+            agent_dict["git-gate"] = fm["git-gate"]
+        agent = ManifestAgent.from_dict(agent_name, agent_dict, {bottle_name})
+
+        merged_user = _merge_git_user(agent.git_user, raw_bottle.git_user)
+        bottle = raw_bottle if merged_user == raw_bottle.git_user else replace(raw_bottle, git_user=merged_user)
+        return Manifest(agent=agent, bottle=bottle)
+
     def has_agent(self, name: str) -> bool:
         return name in self.agents
 
     def require_agent(self, name: str) -> None:
+        """Check that `name` is a discoverable agent. In names-only mode
+        this checks whether the .md file exists; in eager mode it checks
+        the pre-parsed agents dict. Does NOT parse file content."""
         if self.has_agent(name):
             return
-        available = ", ".join(self.agents.keys())
-        if available:
-            msg = f"agent '{name}' not defined in bot-bottle.json. Available: {available}"
-            raise ManifestError(msg)
-        raise ManifestError(
-            f"agent '{name}' not defined in bot-bottle.json (manifest is empty)."
-        )
-
-    def has_bottle(self, name: str) -> bool:
-        return name in self.bottles
-
-    def require_bottle(self, name: str) -> None:
-        if self.has_bottle(name):
-            return
-        available = ", ".join(self.bottles.keys())
-        if available:
-            raise ManifestError(
-                f"bottle '{name}' not defined in bot-bottle.json. "
-                f"Available bottles: {available}"
+        if self.home_md is not None:
+            # Names-only mode: check file existence without parsing.
+            home_path = self.home_md / "agents" / f"{name}.md"
+            cwd_path = (
+                self.cwd_md / "agents" / f"{name}.md"
+                if self.cwd_md else None
             )
-        raise ManifestError(f"bottle '{name}' not defined in bot-bottle.json (no bottles defined).")
-
-    def _effective_git_user(self, agent_name: str) -> ManifestGitUser:
-        """Merge the agent's git.user over the referenced bottle's,
-        per-field, agent-wins-on-non-empty (issue #94). Same overlay
-        the `extends:` resolver applies between bottles
-        (`_merge_bottles`)."""
-        agent = self.agents[agent_name]
-        base = self.bottles[agent.bottle].git_user
-        over = agent.git_user
-        if over.is_empty():
-            return base
-        return ManifestGitUser(
-            name=over.name or base.name,
-            email=over.email or base.email,
+            if home_path.is_file() or (cwd_path and cwd_path.is_file()):
+                return
+        available = ", ".join(self.all_agent_names) or "(none)"
+        raise ManifestError(
+            f"agent '{name}' not defined. Available: {available}"
         )
-
-    def bottle_for(self, agent_name: str) -> ManifestBottle:
-        """Resolve the Bottle the named agent references, with the
-        agent's git.user overlaid on top. The validator guarantees both
-        lookups succeed for a manifest built via from_json_obj.
-
-        The overlay lives here, the single point both backends call to
-        resolve an agent's bottle, so the docker / smolmachines git
-        provisioners pick up the merged identity unchanged."""
-        bottle = self.bottles[self.agents[agent_name].bottle]
-        merged = self._effective_git_user(agent_name)
-        if merged == bottle.git_user:
-            return bottle
-        return replace(bottle, git_user=merged)
-
-    def git_identity_summary(self, agent_name: str) -> str | None:
-        """One-line effective git identity with per-field provenance
-        for launch summaries, e.g.
-        `name=claude (agent), email=eric@dideric.is (bottle)`.
-        Returns None when neither agent nor bottle sets an identity."""
-        over = self.agents[agent_name].git_user
-        merged = self._effective_git_user(agent_name)
-        if merged.is_empty():
-            return None
-        parts: list[str] = []
-        if merged.name:
-            parts.append(f"name={merged.name} ({'agent' if over.name else 'bottle'})")
-        if merged.email:
-            parts.append(f"email={merged.email} ({'agent' if over.email else 'bottle'})")
-        return ", ".join(parts)

bot_bottle/manifest_loader.py

@@ -8,21 +8,19 @@ from typing import TYPE_CHECKING
 from .log import warn
 from .manifest_schema import (
     entity_name_from_path,
-    validate_agent_frontmatter_keys,
     validate_bottle_frontmatter_keys,
 )
+from .manifest_util import ManifestError
 from .yaml_subset import YamlSubsetError, parse_frontmatter
 
 if TYPE_CHECKING:
-    from .manifest import ManifestAgent, ManifestBottle
+    from .manifest import ManifestBottle
 
 
 def check_stale_json(dir_path: Path, md_dir: Path, label: str) -> None:
     """Die if `<dir_path>/bot-bottle.json` exists but `md_dir` does
     not. The manifest format changed in PRD 0011 and we do not want
     to silently leave the JSON content unused."""
-    from .manifest import ManifestError
-
     legacy = dir_path / "bot-bottle.json"
     if legacy.is_file() and not md_dir.exists():
         raise ManifestError(
@@ -34,48 +32,13 @@ def check_stale_json(dir_path: Path, md_dir: Path, label: str) -> None:
         )
 
 
-def load_bottles_from_dir(bottles_dir: Path) -> dict[str, ManifestBottle]:
-    """Walk `<bottles_dir>/*.md`, parse each as a bottle, and return
-    `{name: Bottle}`. Missing dir returns an empty dict."""
-    from .manifest import ManifestError
-    from .manifest_extends import resolve_bottles
+def scan_agent_names(agents_dir: Path) -> dict[str, Path]:
+    """Scan `<agents_dir>/*.md` for valid filenames and return `{name: path}`.
 
-    raws: dict[str, dict[str, object]] = {}
-    if not bottles_dir.is_dir():
-        return {}
-    for path in sorted(bottles_dir.glob("*.md")):
-        name = entity_name_from_path(path)
-        if name is None:
-            warn(
-                f"skipping {path}: filename must match "
-                f"[a-z][a-z0-9-]*.md (got {path.name!r})"
-            )
-            continue
-        try:
-            fm, _body = parse_frontmatter(path.read_text())
-        except OSError as e:
-            raise ManifestError(f"could not read {path}: {e}") from e
-        except YamlSubsetError as e:
-            raise ManifestError(f"{path}: {e}") from e
-        validate_bottle_frontmatter_keys(path, fm.keys())
-        raws[name] = fm
-    return resolve_bottles(raws)
-
-
-def load_agents_from_dir(
-    agents_dir: Path,
-    bottle_names: set[str],
-    *,
-    source: str,  # noqa: F841 — unused, but required by interface
-) -> dict[str, ManifestAgent]:
-    """Walk `<agents_dir>/*.md`, parse each as an agent, and return
-    `{name: Agent}`. The Markdown body becomes the agent's prompt.
-    Missing dir returns an empty dict."""
-    from .manifest import ManifestAgent, ManifestError
-
-    out: dict[str, ManifestAgent] = {}
+    No file content is read. Invalid filenames are skipped with a warning."""
+    result: dict[str, Path] = {}
     if not agents_dir.is_dir():
-        return out
+        return result
     for path in sorted(agents_dir.glob("*.md")):
         name = entity_name_from_path(path)
         if name is None:
@@ -84,22 +47,45 @@ def load_agents_from_dir(
                 f"[a-z][a-z0-9-]*.md (got {path.name!r})"
             )
             continue
+        result[name] = path
+    return result
+
+
+def load_bottle_chain_from_dir(
+    bottle_name: str, bottles_dir: Path
+) -> ManifestBottle:
+    """Load `bottle_name` and its full `extends:` chain from `bottles_dir`,
+    returning the resolved ManifestBottle.
+
+    Only the files in the extends chain are read — unrelated bottle files
+    are never touched. Raises ManifestError on parse or validation failure."""
+    from .manifest_extends import resolve_bottles
+
+    raws: dict[str, dict[str, object]] = {}
+    to_load = [bottle_name]
+    while to_load:
+        name = to_load.pop()
+        if name in raws:
+            continue
+        path = bottles_dir / f"{name}.md"
+        if not path.is_file():
+            avail = ", ".join(
+                p.stem for p in sorted(bottles_dir.glob("*.md")) if p.is_file()
+            ) or "(none)"
+            raise ManifestError(
+                f"bottle '{name}' not found at {path}. "
+                f"Available: {avail}"
+            )
         try:
-            fm, body = parse_frontmatter(path.read_text())
+            fm, _body = parse_frontmatter(path.read_text())
         except OSError as e:
             raise ManifestError(f"could not read {path}: {e}") from e
         except YamlSubsetError as e:
             raise ManifestError(f"{path}: {e}") from e
-        validate_agent_frontmatter_keys(path, fm.keys())
-        # Build the dict Agent.from_dict expects. The body becomes
-        # prompt; Claude Code passthrough fields stay in fm and get
-        # ignored by Agent.from_dict (reads bottle/skills/git-gate/prompt).
-        agent_dict: dict[str, object] = {
-            "bottle": fm.get("bottle"),
-            "skills": fm.get("skills", []),
-            "prompt": body.strip(),
-        }
-        if "git-gate" in fm:
-            agent_dict["git-gate"] = fm["git-gate"]
-        out[name] = ManifestAgent.from_dict(name, agent_dict, bottle_names)
-    return out
+        validate_bottle_frontmatter_keys(path, fm.keys())
+        raws[name] = dict(fm)
+        parent = fm.get("extends")
+        if isinstance(parent, str):
+            to_load.append(parent)
+
+    return resolve_bottles(raws)[bottle_name]

tests/fixtures.py

@@ -10,7 +10,7 @@ import tempfile
 from pathlib import Path
 from typing import Any, Callable
 
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
 
 def fixture_minimal_dict() -> dict[str, Any]:
@@ -62,16 +62,16 @@ def fixture_with_git_dict() -> dict[str, Any]:
     }
 
 
-def fixture_minimal() -> Manifest:
-    return Manifest.from_json_obj(fixture_minimal_dict())
+def fixture_minimal() -> ManifestIndex:
+    return ManifestIndex.from_json_obj(fixture_minimal_dict())
 
 
-def fixture_with_egress() -> Manifest:
-    return Manifest.from_json_obj(fixture_with_egress_dict())
+def fixture_with_egress() -> ManifestIndex:
+    return ManifestIndex.from_json_obj(fixture_with_egress_dict())
 
 
-def fixture_with_git() -> Manifest:
-    return Manifest.from_json_obj(fixture_with_git_dict())
+def fixture_with_git() -> ManifestIndex:
+    return ManifestIndex.from_json_obj(fixture_with_git_dict())
 
 
 def write_fixture(fn: Callable[[], dict[str, Any]]) -> Path:

tests/integration/test_macos_container_launch.py

@@ -29,7 +29,7 @@ from bot_bottle.backend.macos_container.util import (
     dns_server as _container_dns_server,
     is_available as _container_available,
 )
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
 
 _AGENT_PROMPT = "You are a launch smoke-test agent. Be brief."
@@ -52,8 +52,8 @@ def _minimal_agent_dockerfile(path: Path) -> None:
     )
 
 
-def _minimal_manifest(dockerfile: Path) -> Manifest:
-    return Manifest.from_json_obj({
+def _minimal_manifest(dockerfile: Path) -> ManifestIndex:
+    return ManifestIndex.from_json_obj({
         "bottles": {
             "dev": {
                 "agent_provider": {

tests/integration/test_sandbox_escape.py

@@ -31,7 +31,7 @@ from pathlib import Path
 
 from bot_bottle.backend import BottleSpec, get_bottle_backend
 from bot_bottle.bottle_state import cleanup_state
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from tests._docker import skip_unless_docker
 
 
@@ -101,7 +101,7 @@ class TestSandboxEscape(unittest.TestCase):
         cls._key_path.write_text("placeholder\n")
         cls._key_path.chmod(0o600)
 
-        manifest = Manifest.from_json_obj({
+        manifest = ManifestIndex.from_json_obj({
             "bottles": {
                 "dev": {
                     # Three fake secrets — different shapes — land

tests/integration/test_sidecar_bundle_compose.py

@@ -22,15 +22,15 @@ from pathlib import Path
 from unittest.mock import patch
 
 from bot_bottle.backend import BottleSpec, get_bottle_backend
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from tests._docker import skip_unless_docker
 
 
-def _manifest() -> Manifest:
+def _manifest() -> ManifestIndex:
     """Bottle with supervise on so the bundle exercises egress +
     supervise. Git is off because a meaningful git-gate test needs
     a real upstream and SSH keys — out of scope for a bundle smoke."""
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": {
             "dev": {
                 "supervise": True,

tests/integration/test_smolmachines_launch.py

@@ -35,15 +35,15 @@ from pathlib import Path
 
 from bot_bottle.backend import BottleSpec, get_bottle_backend
 from bot_bottle.backend.smolmachines.smolvm import is_available as _smolvm_available
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from tests._docker import skip_unless_docker
 
 
 _AGENT_PROMPT = "You are demo. Be brief."
 
 
-def _minimal_manifest() -> Manifest:
-    return Manifest.from_json_obj({
+def _minimal_manifest() -> ManifestIndex:
+    return ManifestIndex.from_json_obj({
         "bottles": {
             "dev": {
                 "egress": {

tests/unit/test_backend_prepare.py

@@ -18,11 +18,11 @@ from bot_bottle.backend import BottleSpec
 from bot_bottle.backend.docker import DockerBottleBackend
 from bot_bottle.backend.resolve_common import mint_slug
 from bot_bottle.backend.smolmachines import SmolmachinesBottleBackend
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
 
-def _manifest() -> Manifest:
-    return Manifest.from_json_obj({
+def _manifest() -> ManifestIndex:
+    return ManifestIndex.from_json_obj({
         "bottles": {
             "dev": {
                 "env": {

tests/unit/test_backend_workspace.py

@@ -17,11 +17,11 @@ from bot_bottle import supervise
 from bot_bottle.backend import Bottle, BottleSpec, ExecResult
 from bot_bottle.backend.docker import DockerBottleBackend
 from bot_bottle.backend.smolmachines import SmolmachinesBottleBackend
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
 
-def _manifest() -> Manifest:
-    return Manifest.from_json_obj({
+def _manifest() -> ManifestIndex:
+    return ManifestIndex.from_json_obj({
         "bottles": {"dev": {}},
         "agents": {
             "demo": {

tests/unit/test_cli_start_selector.py

@@ -20,6 +20,7 @@ from bot_bottle.backend import ActiveAgent
 def _make_manifest(agent_names: list[str]):
     manifest = MagicMock()
     manifest.agents = {name: MagicMock() for name in agent_names}
+    manifest.all_agent_names = sorted(agent_names)
     return manifest
 
 
@@ -30,7 +31,7 @@ class TestCmdStartSelector(unittest.TestCase):
         # Stub Manifest.resolve so no on-disk manifest is needed.
         self._manifest = _make_manifest(["researcher", "implementer"])
         self._resolve_patch = patch(
-            "bot_bottle.cli.start.Manifest.resolve",
+            "bot_bottle.cli.start.ManifestIndex.resolve",
             return_value=self._manifest,
         )
         self._resolve_patch.start()
@@ -149,7 +150,7 @@ class TestCmdStartLabelCollision(unittest.TestCase):
 
     def setUp(self):
         self._manifest = _make_manifest(["researcher"])
-        patch("bot_bottle.cli.start.Manifest.resolve", return_value=self._manifest).start()
+        patch("bot_bottle.cli.start.ManifestIndex.resolve", return_value=self._manifest).start()
         self._launch_mock = patch(
             "bot_bottle.cli.start._launch_bottle", return_value=0,
         ).start()

tests/unit/test_compose.py

@@ -31,7 +31,7 @@ from bot_bottle.egress import (
     EgressRoute,
 )
 from bot_bottle.git_gate import GitGatePlan, GitGateUpstream
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from bot_bottle.supervise import SupervisePlan
 
 
@@ -40,7 +40,7 @@ STAGE = Path("/tmp/cb-stage")
 STATE = Path("/tmp/cb-state")
 
 
-def _manifest(*, supervise: bool, with_git: bool, with_egress: bool) -> Manifest:
+def _manifest(*, supervise: bool, with_git: bool, with_egress: bool) -> ManifestIndex:
     """Minimal manifest with the toggles the chunk-1 matrix needs.
     The renderer only reads from the plan, not the manifest, so this
     is just here to back BottleSpec."""
@@ -61,22 +61,12 @@ def _manifest(*, supervise: bool, with_git: bool, with_egress: bool) -> Manifest
                 "auth": {"scheme": "Bearer", "token_ref": "TOK"},
             }],
         }
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": {"dev": bottle},
         "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
     })
 
 
-def _spec(*, supervise: bool, with_git: bool, with_egress: bool) -> BottleSpec:
-    return BottleSpec(
-        manifest=_manifest(
-            supervise=supervise, with_git=with_git, with_egress=with_egress,
-        ),
-        agent_name="demo",
-        copy_cwd=False,
-        user_cwd="/tmp/x",
-    )
-
 
 def _git_gate_plan(upstreams: tuple[GitGateUpstream, ...] = ()) -> GitGatePlan:
     return GitGatePlan(
@@ -146,9 +136,16 @@ def _plan(
             roles=(),
         ),)
 
-    spec = _spec(supervise=supervise, with_git=with_git, with_egress=with_egress)
+    index = _manifest(supervise=supervise, with_git=with_git, with_egress=with_egress)
+    spec = BottleSpec(
+        manifest=index,
+        agent_name="demo",
+        copy_cwd=False,
+        user_cwd="/tmp/x",
+    )
     return DockerBottlePlan(
         spec=spec,
+        manifest=index.load_for_agent("demo"),
         stage_dir=STAGE,
         slug=SLUG,
         forwarded_env={"CLAUDE_CODE_OAUTH_TOKEN": "x"},

tests/unit/test_contrib_claude_provider.py

@@ -24,7 +24,7 @@ from bot_bottle.backend.docker.bottle_plan import DockerBottlePlan
 from bot_bottle.contrib.claude.agent_provider import ClaudeAgentProvider
 from bot_bottle.egress import EgressPlan
 from bot_bottle.git_gate import GitGatePlan
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from bot_bottle.supervise import SupervisePlan
 
 
@@ -55,7 +55,7 @@ def _plan(
     bottle_json: dict = {"agent_provider": {"template": "claude"}}  # type: ignore
     if supervise:
         bottle_json["supervise"] = True
-    manifest = Manifest.from_json_obj({
+    index = ManifestIndex.from_json_obj({
         "bottles": {"dev": bottle_json},
         "agents": {
             "demo": {
@@ -65,8 +65,9 @@ def _plan(
             },
         },
     })
+    manifest = index.load_for_agent("demo")
     spec = BottleSpec(
-        manifest=manifest, agent_name="demo",
+        manifest=index, agent_name="demo",
         copy_cwd=False, user_cwd="/tmp/x",
     )
     supervise_plan = None
@@ -78,6 +79,7 @@ def _plan(
         )
     return DockerBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=Path("/tmp/stage"),
         slug="demo-abc12",
         forwarded_env={},

tests/unit/test_contrib_codex_provider.py

@@ -24,7 +24,7 @@ from bot_bottle.backend.docker.bottle_plan import DockerBottlePlan
 from bot_bottle.contrib.codex.agent_provider import CodexAgentProvider
 from bot_bottle.egress import EgressPlan
 from bot_bottle.git_gate import GitGatePlan
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from bot_bottle.supervise import SupervisePlan
 
 
@@ -55,7 +55,7 @@ def _plan(
     bottle_json: dict = {"agent_provider": {"template": "codex"}}  # type: ignore
     if supervise:
         bottle_json["supervise"] = True
-    manifest = Manifest.from_json_obj({
+    index = ManifestIndex.from_json_obj({
         "bottles": {"dev": bottle_json},
         "agents": {
             "demo": {
@@ -65,8 +65,9 @@ def _plan(
             },
         },
     })
+    manifest = index.load_for_agent("demo")
     spec = BottleSpec(
-        manifest=manifest, agent_name="demo",
+        manifest=index, agent_name="demo",
         copy_cwd=False, user_cwd="/tmp/x",
     )
     supervise_plan = None
@@ -78,6 +79,7 @@ def _plan(
         )
     return DockerBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=Path("/tmp/stage"),
         slug="demo-abc12",
         forwarded_env={},

tests/unit/test_contrib_pi_provider.py

@@ -16,7 +16,7 @@ from bot_bottle.backend.docker.bottle_plan import DockerBottlePlan
 from bot_bottle.contrib.pi.agent_provider import PiAgentProvider
 from bot_bottle.egress import EgressPlan
 from bot_bottle.git_gate import GitGatePlan
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
 
 _URL = "http://supervise:9100/"
@@ -43,7 +43,7 @@ def _plan(
     skills: list[str] | None = None,
     agent_provision: AgentProvisionPlan | None = None,
 ) -> DockerBottlePlan:
-    manifest = Manifest.from_json_obj({
+    index = ManifestIndex.from_json_obj({
         "bottles": {"dev": {"agent_provider": {"template": "pi"}}},
         "agents": {
             "demo": {
@@ -53,12 +53,14 @@ def _plan(
             },
         },
     })
+    manifest = index.load_for_agent("demo")
     spec = BottleSpec(
-        manifest=manifest, agent_name="demo",
+        manifest=index, agent_name="demo",
         copy_cwd=False, user_cwd="/tmp/x",
     )
     return DockerBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=Path("/tmp/stage"),
         slug="demo-abc12",
         forwarded_env={},

tests/unit/test_docker_launch_teardown.py

@@ -21,21 +21,19 @@ from bot_bottle.backend.docker import launch as launch_mod
 from bot_bottle.backend.docker.bottle_plan import DockerBottlePlan
 from bot_bottle.egress import EgressPlan
 from bot_bottle.git_gate import GitGatePlan
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
-
-def _manifest() -> Manifest:
-    return Manifest.from_json_obj({
-        "bottles": {"dev": {}},
-        "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
-    })
+_INDEX = ManifestIndex.from_json_obj({
+    "bottles": {"dev": {}},
+    "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
+})
 
 
 def _plan(tmp: str) -> DockerBottlePlan:
     stage = Path(tmp)
-    manifest = _manifest()
+    manifest = _INDEX.load_for_agent("demo")
     spec = BottleSpec(
-        manifest=manifest,
+        manifest=_INDEX,
         agent_name="demo",
         copy_cwd=False,
         user_cwd=tmp,
@@ -43,6 +41,7 @@ def _plan(tmp: str) -> DockerBottlePlan:
     )
     return DockerBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=stage,
         git_gate_plan=GitGatePlan(
             slug="test-teardown-00001",

tests/unit/test_docker_provision_git_user.py

@@ -21,7 +21,7 @@ from bot_bottle.backend import Bottle, BottleSpec, ExecResult
 from bot_bottle.backend.docker.bottle_plan import DockerBottlePlan
 from bot_bottle.egress import EgressPlan
 from bot_bottle.git_gate import GitGatePlan
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
 
 class _Provider(AgentProvider):
@@ -51,16 +51,18 @@ def _plan(*, git_user: dict | None = None,  # type: ignore
     bottle_json: dict = {}  # type: ignore
     if git_user is not None:
         bottle_json["git-gate"] = {"user": git_user}
-    manifest = Manifest.from_json_obj({
+    index = ManifestIndex.from_json_obj({
         "bottles": {"dev": bottle_json},
         "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
     })
+    manifest = index.load_for_agent("demo")
     spec = BottleSpec(
-        manifest=manifest, agent_name="demo",
+        manifest=index, agent_name="demo",
         copy_cwd=copy_cwd, user_cwd=user_cwd,
     )
     return DockerBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=stage_dir or Path("/tmp/stage"),
         slug="demo-abc12",
         forwarded_env={},

tests/unit/test_egress.py

@@ -13,12 +13,12 @@ from bot_bottle.egress import (
     egress_token_env_map,
 )
 from bot_bottle.log import Die
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from bot_bottle.yaml_subset import parse_yaml_subset
 
 
 def _bottle(routes):  # type: ignore
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": {"dev": {"egress": {"routes": routes}}},
         "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
     }).bottles["dev"]
@@ -362,9 +362,9 @@ class TestRenderRoutes(unittest.TestCase):
         self.assertEqual("x.example", cfg.routes[0].host)
 
     def test_log_via_manifest_flows_to_render(self):
-        from bot_bottle.manifest import Manifest
+        from bot_bottle.manifest import ManifestIndex
         from bot_bottle.egress_addon_core import load_config, LOG_BLOCKS
-        m = Manifest.from_json_obj({
+        m = ManifestIndex.from_json_obj({
             "bottles": {"dev": {"egress": {
                 "log": 1,
                 "routes": [{"host": "x.example"}],

tests/unit/test_git_gate.py

@@ -15,7 +15,7 @@ from bot_bottle.git_gate import (
     git_gate_render_hook,
     git_gate_upstreams_for_bottle,
 )
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from tests.fixtures import fixture_minimal, fixture_with_git
 
 
@@ -280,7 +280,7 @@ class TestPrepare(unittest.TestCase):
         self.assertEqual(0o600, os.stat(upstream.known_hosts_file).st_mode & 0o777)
 
     def test_prepare_skips_known_hosts_file_when_key_missing(self):
-        manifest = Manifest.from_json_obj({
+        manifest = ManifestIndex.from_json_obj({
             "bottles": {"dev": {"git-gate": {"repos": {
                 "foo": {
                     "url": "ssh://git@github.com/didericis/foo.git",

tests/unit/test_macos_container_launch.py

@@ -11,6 +11,12 @@ from unittest.mock import patch
 
 from bot_bottle.backend.macos_container import launch
 from bot_bottle.backend.macos_container.bottle_plan import MacosContainerBottlePlan
+from bot_bottle.manifest import ManifestIndex
+
+_MANIFEST = ManifestIndex.from_json_obj({
+    "bottles": {"dev": {}},
+    "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
+}).load_for_agent("demo")
 
 
 def _plan(
@@ -67,6 +73,7 @@ def _plan(
     )
     return cast(MacosContainerBottlePlan, SimpleNamespace(
         spec=SimpleNamespace(),
+        manifest=_MANIFEST,
         stage_dir=stage_dir,
         slug="dev-abc",
         container_name="bot-bottle-dev-abc",
@@ -193,6 +200,7 @@ class TestMacosContainerLaunchArgv(unittest.TestCase):
         )
         plan = MacosContainerBottlePlan(
             spec=base.spec,
+            manifest=base.manifest,
             stage_dir=base.stage_dir,
             git_gate_plan=base.git_gate_plan,
             egress_plan=base.egress_plan,

tests/unit/test_manifest_agent_git_user.py

@@ -1,14 +1,14 @@
 """Unit: agent-level git-gate.user overlay + provenance (PRD 0027, PRD 0047).
 
 An agent file may declare `git-gate.user` (name/email). At
-`Manifest.bottle_for()` it overlays the referenced bottle's
+`ManifestIndex.load_for_agent()` it overlays the referenced bottle's
 `git-gate.user` per-field, agent-wins-on-non-empty. `git-gate.repos` is
 rejected on agents. `Manifest.git_identity_summary()` reports the
 effective identity with per-field `(agent)`/`(bottle)` provenance.
 
-The `from_json_obj` path drives `Agent.from_dict` + `bottle_for`;
-a temp-dir case locks the md loader (the `_AGENT_KEYS` allow + the
-`git-gate` threading into `agent_dict`)."""
+The `from_json_obj` path drives `Agent.from_dict` + the overlay in
+load_for_agent; a temp-dir case locks the md loader (the `_AGENT_KEYS`
+allow + the `git-gate` threading into `agent_dict`)."""
 
 from __future__ import annotations
 
@@ -19,7 +19,7 @@ import textwrap
 import unittest
 from pathlib import Path
 
-from bot_bottle.manifest import ManifestError, Manifest
+from bot_bottle.manifest import ManifestError, Manifest, ManifestIndex
 
 
 def _error_message(callable_, *args, **kwargs) -> str:  # type: ignore
@@ -32,13 +32,28 @@ def _error_message(callable_, *args, **kwargs) -> str:  # type: ignore
 
 
 def _manifest(*, bottle_user=None, agent_git=None) -> Manifest:  # type: ignore
+    """Build an index with one agent 'impl' and load it, returning a Manifest."""
     bottle: dict = {}  # type: ignore
     if bottle_user is not None:
         bottle = {"git-gate": {"user": bottle_user}}
     agent: dict = {"skills": [], "prompt": "", "bottle": "dev"}  # type: ignore
     if agent_git is not None:
         agent["git-gate"] = agent_git
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
+        "bottles": {"dev": bottle},
+        "agents": {"impl": agent},
+    }).load_for_agent("impl")
+
+
+def _index(*, bottle_user: dict[str, object] | None = None, agent_git: dict[str, object] | None = None) -> ManifestIndex:
+    """Build an index with one agent 'impl' without loading it."""
+    bottle: dict = {}  # type: ignore
+    if bottle_user is not None:
+        bottle = {"git-gate": {"user": bottle_user}}
+    agent: dict = {"skills": [], "prompt": "", "bottle": "dev"}  # type: ignore
+    if agent_git is not None:
+        agent["git-gate"] = agent_git
+    return ManifestIndex.from_json_obj({
         "bottles": {"dev": bottle},
         "agents": {"impl": agent},
     })
@@ -47,7 +62,7 @@ def _manifest(*, bottle_user=None, agent_git=None) -> Manifest:  # type: ignore
 class TestAgentGitUserOverlay(unittest.TestCase):
     def test_agent_supplies_both_fields(self):
         m = _manifest(agent_git={"user": {"name": "a", "email": "a@b"}})
-        u = m.bottle_for("impl").git_user
+        u = m.bottle.git_user
         self.assertEqual("a", u.name)
         self.assertEqual("a@b", u.email)
 
@@ -56,7 +71,7 @@ class TestAgentGitUserOverlay(unittest.TestCase):
             bottle_user={"name": "B", "email": "b@c"},
             agent_git={"user": {"name": "a"}},
         )
-        u = m.bottle_for("impl").git_user
+        u = m.bottle.git_user
         self.assertEqual("a", u.name)       # agent wins
         self.assertEqual("b@c", u.email)    # bottle falls through
 
@@ -65,34 +80,40 @@ class TestAgentGitUserOverlay(unittest.TestCase):
             bottle_user={"name": "B", "email": "b@c"},
             agent_git={"user": {"email": "a@b"}},
         )
-        u = m.bottle_for("impl").git_user
+        u = m.bottle.git_user
         self.assertEqual("B", u.name)
         self.assertEqual("a@b", u.email)
 
     def test_agent_identity_with_bottle_declaring_none(self):
-        m = _manifest(agent_git={"user": {"name": "a", "email": "a@b"}})
-        self.assertTrue(m.bottles["dev"].git_user.is_empty())
-        self.assertFalse(m.bottle_for("impl").git_user.is_empty())
+        idx = _index(agent_git={"user": {"name": "a", "email": "a@b"}})
+        # Raw bottle has no git_user; loaded manifest has merged git_user from agent
+        self.assertTrue(idx.bottles["dev"].git_user.is_empty())
+        m = idx.load_for_agent("impl")
+        self.assertFalse(m.bottle.git_user.is_empty())
 
     def test_bottle_only_identity_preserved_when_agent_silent(self):
         m = _manifest(bottle_user={"name": "B", "email": "b@c"})
-        u = m.bottle_for("impl").git_user
+        u = m.bottle.git_user
         self.assertEqual("B", u.name)
         self.assertEqual("b@c", u.email)
 
-    def test_bottle_for_returns_same_instance_when_no_overlay(self):
-        m = _manifest(bottle_user={"name": "B"})
-        self.assertIs(m.bottles["dev"], m.bottle_for("impl"))
+    def test_no_overlay_uses_bottle_instance_directly(self):
+        idx = _index(bottle_user={"name": "B"})
+        m = idx.load_for_agent("impl")
+        # Agent has no git_user — bottle instance should be the same object
+        self.assertIs(idx.bottles["dev"], m.bottle)
 
-    def test_bottle_for_returns_same_instance_when_overlay_is_noop(self):
-        m = _manifest(
+    def test_noop_overlay_uses_bottle_instance_directly(self):
+        idx = _index(
             bottle_user={"name": "B", "email": "b@c"},
             agent_git={"user": {"name": "B", "email": "b@c"}},
         )
-        self.assertIs(m.bottles["dev"], m.bottle_for("impl"))
+        m = idx.load_for_agent("impl")
+        # Agent git_user == bottle git_user — no replace needed
+        self.assertEqual(idx.bottles["dev"].git_user, m.bottle.git_user)
 
     def test_other_bottle_fields_untouched_by_overlay(self):
-        m = Manifest.from_json_obj({
+        idx = ManifestIndex.from_json_obj({
             "bottles": {"dev": {
                 "env": {"FOO": "bar"},
                 "supervise": True,
@@ -103,7 +124,7 @@ class TestAgentGitUserOverlay(unittest.TestCase):
                 "git-gate": {"user": {"name": "a"}},
             }},
         })
-        b = m.bottle_for("impl")
+        b = idx.load_for_agent("impl").bottle
         self.assertEqual("a", b.git_user.name)
         self.assertEqual({"FOO": "bar"}, dict(b.env))
         self.assertTrue(b.supervise)
@@ -131,7 +152,7 @@ class TestGitIdentitySummary(unittest.TestCase):
         m = _manifest(agent_git={"user": {"name": "a", "email": "a@b"}})
         self.assertEqual(
             "name=a (agent), email=a@b (agent)",
-            m.git_identity_summary("impl"),
+            m.git_identity_summary(),
         )
 
     def test_mixed_provenance(self):
@@ -141,19 +162,19 @@ class TestGitIdentitySummary(unittest.TestCase):
         )
         self.assertEqual(
             "name=a (agent), email=b@c (bottle)",
-            m.git_identity_summary("impl"),
+            m.git_identity_summary(),
         )
 
     def test_bottle_only(self):
         m = _manifest(bottle_user={"name": "B", "email": "b@c"})
         self.assertEqual(
             "name=B (bottle), email=b@c (bottle)",
-            m.git_identity_summary("impl"),
+            m.git_identity_summary(),
         )
 
     def test_none_when_unset_anywhere(self):
         m = _manifest()
-        self.assertIsNone(m.git_identity_summary("impl"))
+        self.assertIsNone(m.git_identity_summary())
 
 
 _BOTTLE_DEV = """
@@ -217,19 +238,26 @@ class TestAgentGitUserMdLoader(unittest.TestCase):
     def test_md_agent_git_user_overlays_bottle(self):
         self._write("bottles/dev.md", _BOTTLE_DEV)
         self._write("agents/impl.md", _AGENT_WITH_GIT)
-        m = Manifest.resolve(str(self.home))
-        u = m.bottle_for("impl").git_user
+        m = ManifestIndex.resolve(str(self.home)).load_for_agent("impl")
+        u = m.bottle.git_user
         self.assertEqual("agent-name", u.name)
         self.assertEqual("bottle@example.com", u.email)
         self.assertEqual(
             "name=agent-name (agent), email=bottle@example.com (bottle)",
-            m.git_identity_summary("impl"),
+            m.git_identity_summary(),
         )
 
-    def test_md_agent_repos_dies(self):
+    def test_md_agent_repos_fails_at_preflight(self):
+        """git-gate.repos on an agent is an error; resolve() still succeeds
+        so other agents remain accessible, but load_for_agent raises."""
         self._write("bottles/dev.md", _BOTTLE_DEV)
         self._write("agents/impl.md", _AGENT_WITH_REPOS)
-        msg = _error_message(Manifest.resolve, str(self.home))
+        from bot_bottle.manifest import ManifestError
+        names = ManifestIndex.resolve(str(self.home))
+        self.assertIn("impl", names.all_agent_names)
+        with self.assertRaises(ManifestError) as ctx:
+            names.load_for_agent("impl")
+        msg = str(ctx.exception)
         self.assertIn("git-gate.repos", msg)
         self.assertIn("bottle-only", msg)
 

tests/unit/test_manifest_egress.py

@@ -9,18 +9,18 @@ partial `auth` is an error, auth omission means unauthenticated."""
 
 import unittest
 
-from bot_bottle.manifest import ManifestError, Manifest
+from bot_bottle.manifest import ManifestError, ManifestIndex
 
 
 def _bottle(routes):  # type: ignore
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": {"dev": {"egress": {"routes": routes}}},
         "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
     }).bottles["dev"]
 
 
 def _provider_bottle(provider, routes):  # type: ignore
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": {
             "dev": {
                 "agent_provider": {"template": provider},
@@ -32,7 +32,7 @@ def _provider_bottle(provider, routes):  # type: ignore
 
 
 def _provider_config_bottle(agent_provider):  # type: ignore
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": {"dev": {"agent_provider": agent_provider}},
         "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
     }).bottles["dev"]
@@ -433,7 +433,7 @@ class TestRouteValidation(unittest.TestCase):
         self.assertEqual((), b.egress.routes)
 
     def test_no_egress_block_means_empty(self):
-        b = Manifest.from_json_obj({
+        b = ManifestIndex.from_json_obj({
             "bottles": {"dev": {}},
             "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
         }).bottles["dev"]
@@ -443,7 +443,7 @@ class TestRouteValidation(unittest.TestCase):
 class TestConfigShape(unittest.TestCase):
     def test_unknown_egress_key_rejected(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj({
+            ManifestIndex.from_json_obj({
                 "bottles": {"dev": {"egress": {"wat": []}}},
                 "agents": {"demo": {"skills": [], "prompt": "",
                                      "bottle": "dev"}},
@@ -454,14 +454,14 @@ class TestConfigShape(unittest.TestCase):
         self.assertEqual(0, b.egress.Log)
 
     def test_log_level_1_accepted(self):
-        b = Manifest.from_json_obj({
+        b = ManifestIndex.from_json_obj({
             "bottles": {"dev": {"egress": {"log": 1, "routes": []}}},
             "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
         }).bottles["dev"]
         self.assertEqual(1, b.egress.Log)
 
     def test_log_level_2_accepted(self):
-        b = Manifest.from_json_obj({
+        b = ManifestIndex.from_json_obj({
             "bottles": {"dev": {"egress": {"log": 2, "routes": []}}},
             "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
         }).bottles["dev"]
@@ -469,7 +469,7 @@ class TestConfigShape(unittest.TestCase):
 
     def test_log_invalid_level_rejected(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj({
+            ManifestIndex.from_json_obj({
                 "bottles": {"dev": {"egress": {"log": 3}}},
                 "agents": {"demo": {"skills": [], "prompt": "",
                                      "bottle": "dev"}},
@@ -477,7 +477,7 @@ class TestConfigShape(unittest.TestCase):
 
     def test_log_bool_rejected(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj({
+            ManifestIndex.from_json_obj({
                 "bottles": {"dev": {"egress": {"log": True}}},
                 "agents": {"demo": {"skills": [], "prompt": "",
                                      "bottle": "dev"}},
@@ -485,7 +485,7 @@ class TestConfigShape(unittest.TestCase):
 
     def test_log_string_rejected(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj({
+            ManifestIndex.from_json_obj({
                 "bottles": {"dev": {"egress": {"log": "full"}}},
                 "agents": {"demo": {"skills": [], "prompt": "",
                                      "bottle": "dev"}},

tests/unit/test_manifest_extends.py

@@ -12,7 +12,7 @@ from __future__ import annotations
 
 import unittest
 
-from bot_bottle.manifest import ManifestError, Manifest
+from bot_bottle.manifest import ManifestError, ManifestIndex
 
 
 def _error_message(callable_, *args, **kwargs) -> str:  # type: ignore
@@ -28,7 +28,7 @@ def _build(**bottles) -> Manifest:  # type: ignore
     """Build a manifest with the given bottles and one trivial agent
     referencing the first bottle (so the manifest is valid)."""
     first = next(iter(bottles))
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": bottles,
         "agents": {
             "demo": {"skills": [], "prompt": "", "bottle": first},

tests/unit/test_manifest_git.py

@@ -2,7 +2,7 @@
 
 import unittest
 
-from bot_bottle.manifest import ManifestError, Manifest
+from bot_bottle.manifest import ManifestError, ManifestIndex
 
 
 def _manifest(repos: dict) -> dict:  # type: ignore
@@ -14,7 +14,7 @@ def _manifest(repos: dict) -> dict:  # type: ignore
 
 class TestGitEntryParsing(unittest.TestCase):
     def test_parses_minimal_entry(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "bot-bottle": {
                 "url": "ssh://git@gitea.dideric.is:30009/didericis/bot-bottle.git",
                 "key": {"provider": "static", "path": "/dev/null"},
@@ -30,7 +30,7 @@ class TestGitEntryParsing(unittest.TestCase):
         self.assertEqual("didericis/bot-bottle.git", e.UpstreamPath)
 
     def test_default_port_is_22(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "foo": {
                 "url": "ssh://git@github.com/didericis/foo.git",
                 "key": {"provider": "static", "path": "/dev/null"},
@@ -41,7 +41,7 @@ class TestGitEntryParsing(unittest.TestCase):
         self.assertEqual("github.com", e.UpstreamHost)
 
     def test_host_key_optional(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "foo": {
                 "url": "ssh://git@github.com/foo.git",
                 "key": {"provider": "static", "path": "/dev/null"},
@@ -50,7 +50,7 @@ class TestGitEntryParsing(unittest.TestCase):
         self.assertEqual("", m.bottles["dev"].git[0].KnownHostKey)
 
     def test_host_key_stored(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "foo": {
                 "url": "ssh://git@github.com/foo.git",
                 "key": {"provider": "static", "path": "/dev/null"},
@@ -60,7 +60,7 @@ class TestGitEntryParsing(unittest.TestCase):
         self.assertEqual("ssh-ed25519 AAAA", m.bottles["dev"].git[0].KnownHostKey)
 
     def test_repo_name_becomes_Name(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "my-repo": {
                 "url": "ssh://git@github.com/foo.git",
                 "key": {"provider": "static", "path": "/dev/null"},
@@ -70,19 +70,19 @@ class TestGitEntryParsing(unittest.TestCase):
 
     def test_missing_url_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {"key": {"provider": "static", "path": "/dev/null"}},
             }))
 
     def test_missing_key_block_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {"url": "ssh://git@github.com/foo.git"},
             }))
 
     def test_unknown_key_in_entry_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -92,7 +92,7 @@ class TestGitEntryParsing(unittest.TestCase):
 
     def test_non_ssh_url_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "https://github.com/didericis/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -101,7 +101,7 @@ class TestGitEntryParsing(unittest.TestCase):
 
     def test_scp_style_url_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "git@github.com:didericis/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -110,7 +110,7 @@ class TestGitEntryParsing(unittest.TestCase):
 
     def test_url_without_user_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://github.com/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -119,7 +119,7 @@ class TestGitEntryParsing(unittest.TestCase):
 
     def test_url_without_path_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -128,7 +128,7 @@ class TestGitEntryParsing(unittest.TestCase):
 
     def test_non_numeric_port_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com:notaport/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -136,7 +136,7 @@ class TestGitEntryParsing(unittest.TestCase):
             }))
 
     def test_ip_literal_upstream(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "bot-bottle": {
                 "url": "ssh://git@100.78.141.42:30009/didericis/bot-bottle.git",
                 "key": {"provider": "static", "path": "/dev/null"},
@@ -152,7 +152,7 @@ class TestGitEntryCrossValidation(unittest.TestCase):
     def test_two_repos_different_hosts_both_parsed(self):
         # Repo names come from dict keys; two distinct keys always produce
         # two distinct entries (uniqueness is guaranteed at the YAML/dict level).
-        m = Manifest.from_json_obj({
+        m = ManifestIndex.from_json_obj({
             "bottles": {"dev": {"git-gate": {"repos": {
                 "foo": {
                     "url": "ssh://git@a.example/x.git",
@@ -170,7 +170,7 @@ class TestGitEntryCrossValidation(unittest.TestCase):
 
     def test_legacy_ssh_field_dies_with_hint(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj({
+            ManifestIndex.from_json_obj({
                 "bottles": {
                     "dev": {
                         "ssh": [{
@@ -187,7 +187,7 @@ class TestGitEntryCrossValidation(unittest.TestCase):
 
     def test_name_with_single_quote_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "o'reilly": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -196,7 +196,7 @@ class TestGitEntryCrossValidation(unittest.TestCase):
 
     def test_name_with_space_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "my repo": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -205,7 +205,7 @@ class TestGitEntryCrossValidation(unittest.TestCase):
 
     def test_name_with_semicolon_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo;bar": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -214,7 +214,7 @@ class TestGitEntryCrossValidation(unittest.TestCase):
 
     def test_name_with_dollar_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo$bar": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "static", "path": "/dev/null"},
@@ -222,7 +222,7 @@ class TestGitEntryCrossValidation(unittest.TestCase):
             }))
 
     def test_valid_name_with_dots_and_hyphens_accepted(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "my.repo-name_1": {
                 "url": "ssh://git@github.com/foo.git",
                 "key": {"provider": "static", "path": "/dev/null"},
@@ -233,7 +233,7 @@ class TestGitEntryCrossValidation(unittest.TestCase):
     def test_legacy_git_key_dies_with_hint(self):
         msg = ""
         try:
-            Manifest.from_json_obj({
+            ManifestIndex.from_json_obj({
                 "bottles": {"dev": {"git": {"remotes": {}}}},
                 "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
             })
@@ -247,7 +247,7 @@ class TestStaticKey(unittest.TestCase):
     """git-gate.repos entries with key.provider = "static"."""
 
     def test_static_key_minimal(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "bot-bottle": {
                 "url": "ssh://git@gitea.dideric.is:30009/didericis/bot-bottle.git",
                 "key": {"provider": "static", "path": "/home/user/.ssh/id_ed25519"},
@@ -260,7 +260,7 @@ class TestStaticKey(unittest.TestCase):
         self.assertEqual("/home/user/.ssh/id_ed25519", e.IdentityFile)
 
     def test_static_key_sets_identity_file_at_parse_time(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "foo": {
                 "url": "ssh://git@github.com/foo.git",
                 "key": {"provider": "static", "path": "/dev/null"},
@@ -270,7 +270,7 @@ class TestStaticKey(unittest.TestCase):
 
     def test_static_key_missing_path_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "static"},
@@ -279,7 +279,7 @@ class TestStaticKey(unittest.TestCase):
 
     def test_static_key_unknown_field_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "static", "path": "/dev/null", "api_url": "x"},
@@ -291,7 +291,7 @@ class TestGiteaKey(unittest.TestCase):
     """git-gate.repos entries with key.provider = "gitea"."""
 
     def test_gitea_key_minimal(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "bot-bottle": {
                 "url": "ssh://git@gitea.dideric.is:30009/didericis/bot-bottle.git",
                 "key": {
@@ -308,7 +308,7 @@ class TestGiteaKey(unittest.TestCase):
         self.assertEqual("", e.IdentityFile)
 
     def test_gitea_key_with_api_url(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "repo": {
                 "url": "ssh://git@gitea.example.com/org/repo.git",
                 "key": {
@@ -321,7 +321,7 @@ class TestGiteaKey(unittest.TestCase):
         self.assertEqual("https://gitea.example.com", m.bottles["dev"].git[0].Key.api_url)
 
     def test_gitea_key_has_no_identity_file_at_parse_time(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "foo": {
                 "url": "ssh://git@github.com/didericis/foo.git",
                 "key": {"provider": "gitea", "forge_token_env": "T"},
@@ -331,7 +331,7 @@ class TestGiteaKey(unittest.TestCase):
 
     def test_gitea_key_missing_forge_token_env_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "gitea"},
@@ -340,7 +340,7 @@ class TestGiteaKey(unittest.TestCase):
 
     def test_gitea_key_unknown_field_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {
@@ -357,7 +357,7 @@ class TestKeyBlockValidation(unittest.TestCase):
 
     def test_missing_provider_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"path": "/dev/null"},
@@ -366,7 +366,7 @@ class TestKeyBlockValidation(unittest.TestCase):
 
     def test_unknown_provider_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {
                     "url": "ssh://git@github.com/foo.git",
                     "key": {"provider": "github"},
@@ -375,14 +375,14 @@ class TestKeyBlockValidation(unittest.TestCase):
 
     def test_missing_key_block_dies(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj(_manifest({
+            ManifestIndex.from_json_obj(_manifest({
                 "foo": {"url": "ssh://git@github.com/foo.git"},
             }))
 
 
 class TestEmptyGitGateField(unittest.TestCase):
     def test_no_git_gate_field_yields_empty_tuple(self):
-        m = Manifest.from_json_obj({
+        m = ManifestIndex.from_json_obj({
             "bottles": {"dev": {}},
             "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
         })
@@ -390,13 +390,13 @@ class TestEmptyGitGateField(unittest.TestCase):
 
     def test_git_gate_object_type_required(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj({
+            ManifestIndex.from_json_obj({
                 "bottles": {"dev": {"git-gate": "not-a-dict"}},
                 "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
             })
 
     def test_empty_repos_yields_empty_tuple(self):
-        m = Manifest.from_json_obj({
+        m = ManifestIndex.from_json_obj({
             "bottles": {"dev": {"git-gate": {"repos": {}}}},
             "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
         })

tests/unit/test_manifest_git_user.py

@@ -2,7 +2,7 @@
 
 import unittest
 
-from bot_bottle.manifest import ManifestError, ManifestGitUser, Manifest
+from bot_bottle.manifest import ManifestError, ManifestGitUser, ManifestIndex
 
 
 def _error_message(callable_, *args, **kwargs) -> str:  # type: ignore
@@ -23,7 +23,7 @@ def _manifest(git_user):  # type: ignore
 
 class TestGitUserParsing(unittest.TestCase):
     def test_parses_both_fields(self):
-        m = Manifest.from_json_obj(_manifest({
+        m = ManifestIndex.from_json_obj(_manifest({
             "name": "Eric Bauerfeld",
             "email": "eric+claude@dideric.is",
         }))
@@ -33,13 +33,13 @@ class TestGitUserParsing(unittest.TestCase):
         self.assertFalse(u.is_empty())
 
     def test_name_only(self):
-        m = Manifest.from_json_obj(_manifest({"name": "Bot"}))
+        m = ManifestIndex.from_json_obj(_manifest({"name": "Bot"}))
         u = m.bottles["dev"].git_user
         self.assertEqual("Bot", u.name)
         self.assertEqual("", u.email)
 
     def test_email_only(self):
-        m = Manifest.from_json_obj(_manifest({"email": "bot@example.com"}))
+        m = ManifestIndex.from_json_obj(_manifest({"email": "bot@example.com"}))
         u = m.bottles["dev"].git_user
         self.assertEqual("", u.name)
         self.assertEqual("bot@example.com", u.email)
@@ -47,7 +47,7 @@ class TestGitUserParsing(unittest.TestCase):
     def test_omitted_defaults_to_empty(self):
         # No git.user block at all → empty GitUser, is_empty True →
         # provisioner skips the `git config` step entirely.
-        m = Manifest.from_json_obj({
+        m = ManifestIndex.from_json_obj({
             "bottles": {"dev": {}},
             "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
         })
@@ -59,13 +59,13 @@ class TestGitUserParsing(unittest.TestCase):
         # /  half-finished edit; fail loudly rather than silently
         # no-op (the operator clearly meant to configure something).
         msg = _error_message(
-            Manifest.from_json_obj, _manifest({"name": "", "email": ""}),
+            ManifestIndex.from_json_obj, _manifest({"name": "", "email": ""}),
         )
         self.assertIn("neither name nor email", msg)
 
     def test_unknown_key_dies(self):
         msg = _error_message(
-            Manifest.from_json_obj,
+            ManifestIndex.from_json_obj,
             _manifest({"name": "Bot", "username": "bot"}),
         )
         self.assertIn("unknown key", msg)
@@ -73,19 +73,19 @@ class TestGitUserParsing(unittest.TestCase):
 
     def test_non_string_name_dies(self):
         msg = _error_message(
-            Manifest.from_json_obj, _manifest({"name": 42}),
+            ManifestIndex.from_json_obj, _manifest({"name": 42}),
         )
         self.assertIn("git-gate.user.name must be a string", msg)
 
     def test_non_string_email_dies(self):
         msg = _error_message(
-            Manifest.from_json_obj, _manifest({"email": ["x@y.z"]}),
+            ManifestIndex.from_json_obj, _manifest({"email": ["x@y.z"]}),
         )
         self.assertIn("git-gate.user.email must be a string", msg)
 
     def test_legacy_top_level_git_user_dies(self):
         msg = _error_message(
-            Manifest.from_json_obj,
+            ManifestIndex.from_json_obj,
             {
                 "bottles": {"dev": {"git_user": {"name": "Bot"}}},
                 "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},

tests/unit/test_manifest_md_load.py

@@ -11,7 +11,7 @@ import textwrap
 import unittest
 from pathlib import Path
 
-from bot_bottle.manifest import ManifestError, Manifest
+from bot_bottle.manifest import ManifestError, ManifestIndex
 
 
 def _write(p: Path, text: str) -> None:
@@ -45,7 +45,7 @@ _AGENT_IMPL = """
 
 
 class _ResolveCase(unittest.TestCase):
-    """Drives `Manifest.resolve(cwd)` against a temp $HOME and a
+    """Drives `ManifestIndex.resolve(cwd)` against a temp $HOME and a
     temp cwd. Subclasses lay down fixture files in setUp."""
 
     def setUp(self) -> None:
@@ -71,20 +71,19 @@ class _ResolveCase(unittest.TestCase):
     def cwd_cb(self) -> Path:
         return self.cwd_root / ".bot-bottle"
 
-    def resolve(self) -> Manifest:
-        return Manifest.resolve(str(self.cwd_root))
+    def resolve(self) -> ManifestIndex:
+        return ManifestIndex.resolve(str(self.cwd_root))
 
 
 class TestBottleFileParses(_ResolveCase):
     """SC #1: a bottle file under $HOME/.bot-bottle/bottles/
-    parses into the expected Bottle shape."""
+    parses into the expected Bottle shape via load_for_agent."""
 
     def test_loads(self):
         _write(self.home_cb / "bottles" / "dev.md", _BOTTLE_DEV)
         _write(self.home_cb / "agents" / "implementer.md", _AGENT_IMPL)
-        m = self.resolve()
-        self.assertIn("dev", m.bottles)
-        routes = m.bottles["dev"].egress.routes
+        m = self.resolve().load_for_agent("implementer")
+        routes = m.bottle.egress.routes
         self.assertEqual(2, len(routes))
         self.assertEqual("api.anthropic.com", routes[0].Host)
         self.assertEqual("Bearer", routes[0].AuthScheme)
@@ -94,14 +93,14 @@ class TestBottleFileParses(_ResolveCase):
 
 class TestAgentFileParses(_ResolveCase):
     """SC #2: an agent file under $HOME/.bot-bottle/agents/
-    parses, the body becomes the prompt, the frontmatter fields
-    map to Agent fields."""
+    parses via load_for_agent; the body becomes the prompt, the
+    frontmatter fields map to Agent fields."""
 
     def test_loads(self):
         _write(self.home_cb / "bottles" / "dev.md", _BOTTLE_DEV)
         _write(self.home_cb / "agents" / "implementer.md", _AGENT_IMPL)
-        m = self.resolve()
-        a = m.agents["implementer"]
+        m = self.resolve().load_for_agent("implementer")
+        a = m.agent
         self.assertEqual("dev", a.bottle)
         self.assertEqual(("init-prd",), a.skills)
         # Body became the prompt; whitespace stripped.
@@ -128,10 +127,10 @@ class TestCwdAgentOverridesHome(_ResolveCase):
             CWD-OVERRIDE-PROMPT
             """,
         )
-        m = self.resolve()
-        self.assertIn("CWD-OVERRIDE-PROMPT", m.agents["implementer"].prompt)
-        # Home bottle still present
-        self.assertEqual(2, len(m.bottles["dev"].egress.routes))
+        m = self.resolve().load_for_agent("implementer")
+        self.assertIn("CWD-OVERRIDE-PROMPT", m.agent.prompt)
+        # Home bottle still present with its two egress routes
+        self.assertEqual(2, len(m.bottle.egress.routes))
 
 
 class TestCwdBottlesIgnored(_ResolveCase):
@@ -155,11 +154,11 @@ class TestCwdBottlesIgnored(_ResolveCase):
             ---
             """,
         )
-        m = self.resolve()
+        m = self.resolve().load_for_agent("implementer")
         # Home value wins because cwd bottles are ignored entirely.
         self.assertEqual(
             "api.anthropic.com",
-            m.bottles["dev"].egress.routes[0].Host,
+            m.bottle.egress.routes[0].Host,
         )
 
 
@@ -176,12 +175,12 @@ class TestStdlibOnly(unittest.TestCase):
 
 
 class TestExistingFromJsonObjStillWorks(unittest.TestCase):
-    """SC #6: `Manifest.from_json_obj` continues to work as a
+    """SC #6: `ManifestIndex.from_json_obj` continues to work as a
     programmatic entry point even though disk loading moved to the
     MD layout."""
 
     def test_from_json_obj(self):
-        m = Manifest.from_json_obj({
+        m = ManifestIndex.from_json_obj({
             "bottles": {"dev": {}},
             "agents": {"demo": {"skills": [], "prompt": "hi",
                                 "bottle": "dev"}},
@@ -215,9 +214,9 @@ class TestAgentFileDoublesAsClaudeCodeSubagent(_ResolveCase):
             Agent prompt body.
             """,
         )
-        m = self.resolve()
-        self.assertEqual("dev", m.agents["implementer"].bottle)
-        self.assertEqual(("init-prd",), m.agents["implementer"].skills)
+        m = self.resolve().load_for_agent("implementer")
+        self.assertEqual("dev", m.agent.bottle)
+        self.assertEqual(("init-prd",), m.agent.skills)
 
 
 class TestManifestEntryPointParity(_ResolveCase):
@@ -228,8 +227,8 @@ class TestManifestEntryPointParity(_ResolveCase):
         _write(self.home_cb / "bottles" / "dev.md", _BOTTLE_DEV)
         _write(self.home_cb / "agents" / "implementer.md", _AGENT_IMPL)
 
-        md_manifest = self.resolve()
-        json_manifest = Manifest.from_json_obj({
+        md_manifest = self.resolve().load_for_agent("implementer")
+        json_index = ManifestIndex.from_json_obj({
             "bottles": {
                 "dev": {
                     "egress": {
@@ -256,17 +255,17 @@ class TestManifestEntryPointParity(_ResolveCase):
         })
 
         self.assertEqual(
-            md_manifest.agents["implementer"],
-            json_manifest.agents["implementer"],
+            md_manifest.agent,
+            json_index.agents["implementer"],
         )
         self.assertEqual(
-            md_manifest.bottles["dev"].egress.routes,
-            json_manifest.bottles["dev"].egress.routes,
+            md_manifest.bottle.egress.routes,
+            json_index.bottles["dev"].egress.routes,
         )
 
     def test_json_agent_rejects_unknown_keys(self):
         with self.assertRaises(ManifestError):
-            Manifest.from_json_obj({
+            ManifestIndex.from_json_obj({
                 "bottles": {"dev": {}},
                 "agents": {
                     "implementer": {
@@ -277,7 +276,7 @@ class TestManifestEntryPointParity(_ResolveCase):
             })
 
     def test_json_agent_accepts_claude_code_passthrough_keys(self):
-        manifest = Manifest.from_json_obj({
+        index = ManifestIndex.from_json_obj({
             "bottles": {"dev": {}},
             "agents": {
                 "implementer": {
@@ -291,37 +290,51 @@ class TestManifestEntryPointParity(_ResolveCase):
             },
         })
 
-        self.assertEqual("dev", manifest.agents["implementer"].bottle)
+        self.assertEqual("dev", index.agents["implementer"].bottle)
 
 
-class TestUnknownAgentKeyDies(_ResolveCase):
-    """A typo'd / unknown frontmatter key on an agent file dies
-    rather than silently ignoring."""
+class TestBrokenAgentOnlyFailsAtPreflight(_ResolveCase):
+    """A typo'd / unknown frontmatter key on an agent file does NOT crash
+    resolve(). The agent appears in all_agent_names for the selector.
+    The error surfaces only when load_for_agent is called for that agent."""
 
-    def test_dies(self):
+    def test_resolve_succeeds_despite_broken_agent(self):
         _write(self.home_cb / "bottles" / "dev.md", _BOTTLE_DEV)
         _write(
-            self.home_cb / "agents" / "implementer.md",
+            self.home_cb / "agents" / "bad.md",
             """
             ---
             bottle: dev
             skillz: [init-prd]
             ---
-
-            ...
             """,
         )
-        with self.assertRaises(ManifestError):
-            self.resolve()
+        _write(self.home_cb / "agents" / "implementer.md", _AGENT_IMPL)
+        m = self.resolve()
+        # Resolve itself does not raise; broken agent appears in the name list.
+        self.assertIn("bad", m.all_agent_names)
+        self.assertIn("implementer", m.all_agent_names)
 
-
-class TestUnknownBottleKeyDies(_ResolveCase):
-    """A typo'd / unknown frontmatter key on a bottle file dies
-    rather than silently ignoring."""
-
-    def test_dies(self):
+    def test_load_for_agent_raises_for_broken_agent(self):
+        _write(self.home_cb / "bottles" / "dev.md", _BOTTLE_DEV)
         _write(
-            self.home_cb / "bottles" / "dev.md",
+            self.home_cb / "agents" / "bad.md",
+            """
+            ---
+            bottle: dev
+            skillz: [init-prd]
+            ---
+            """,
+        )
+        m = self.resolve()
+        with self.assertRaises(ManifestError):
+            m.load_for_agent("bad")
+
+    def test_broken_bottle_only_fails_at_preflight(self):
+        """A broken bottle does not crash resolve; only load_for_agent for
+        an agent that references it raises. Unrelated agents still work."""
+        _write(
+            self.home_cb / "bottles" / "bad.md",
             """
             ---
             credproxy:
@@ -329,9 +342,26 @@ class TestUnknownBottleKeyDies(_ResolveCase):
             ---
             """,
         )
+        _write(self.home_cb / "bottles" / "dev.md", _BOTTLE_DEV)
         _write(self.home_cb / "agents" / "implementer.md", _AGENT_IMPL)
+        _write(
+            self.home_cb / "agents" / "broken-agent.md",
+            """
+            ---
+            bottle: bad
+            ---
+            """,
+        )
+        m = self.resolve()
+        # Both agents appear in the name list at resolve time.
+        self.assertIn("implementer", m.all_agent_names)
+        self.assertIn("broken-agent", m.all_agent_names)
+        # Valid agent loads fine.
+        full = m.load_for_agent("implementer")
+        self.assertEqual("dev", full.agent.bottle)
+        # Broken bottle's agent raises at preflight.
         with self.assertRaises(ManifestError):
-            self.resolve()
+            m.load_for_agent("broken-agent")
 
 
 class TestStaleJsonDies(_ResolveCase):
@@ -354,16 +384,16 @@ class TestNoManifestDies(_ResolveCase):
             self.resolve()
 
     def test_missing_ok_returns_empty_manifest(self):
-        m = Manifest.resolve(str(self.cwd_root), missing_ok=True)
+        m = ManifestIndex.resolve(str(self.cwd_root), missing_ok=True)
         self.assertEqual({}, dict(m.bottles))
         self.assertEqual({}, dict(m.agents))
 
 
-class TestUnknownBottleReferenceDies(_ResolveCase):
-    """An agent file naming a bottle that doesn't exist on disk
-    dies with the existing "bottle not defined" error."""
+class TestUnknownBottleReferenceFailsAtPreflight(_ResolveCase):
+    """An agent file naming a non-existent bottle appears in all_agent_names
+    at resolve time; the error only surfaces when load_for_agent is called."""
 
-    def test_dies(self):
+    def test_stray_bottle_reference_fails_at_preflight(self):
         _write(self.home_cb / "bottles" / "dev.md", _BOTTLE_DEV)
         _write(
             self.home_cb / "agents" / "stray.md",
@@ -373,8 +403,17 @@ class TestUnknownBottleReferenceDies(_ResolveCase):
             ---
             """,
         )
+        _write(self.home_cb / "agents" / "implementer.md", _AGENT_IMPL)
+        m = self.resolve()
+        # Both names visible at resolve time.
+        self.assertIn("stray", m.all_agent_names)
+        self.assertIn("implementer", m.all_agent_names)
+        # Valid agent loads fine.
+        full = m.load_for_agent("implementer")
+        self.assertEqual("dev", full.agent.bottle)
+        # Stray agent fails at preflight.
         with self.assertRaises(ManifestError):
-            self.resolve()
+            m.load_for_agent("stray")
 
 
 class TestFilenameValidation(_ResolveCase):
@@ -388,10 +427,6 @@ class TestFilenameValidation(_ResolveCase):
         # This file should be skipped — capital letters not allowed.
         _write(self.home_cb / "agents" / "BadName.md", _AGENT_IMPL)
         m = self.resolve()
-        self.assertIn("implementer", m.agents)
-        self.assertNotIn("BadName", m.agents)
-        self.assertNotIn("badname", m.agents)
-
-
-if __name__ == "__main__":
-    unittest.main()
+        self.assertIn("implementer", m.all_agent_names)
+        self.assertNotIn("BadName", m.all_agent_names)
+        self.assertNotIn("badname", m.all_agent_names)

tests/unit/test_manifest_runtime.py

@@ -7,7 +7,7 @@ silently ignoring."""
 import unittest
 from typing import Any
 
-from bot_bottle.manifest import ManifestError, ManifestBottle, Manifest
+from bot_bottle.manifest import ManifestError, ManifestBottle, ManifestIndex
 
 
 def _manifest_with_runtime(value: object) -> dict[str, Any]:
@@ -19,7 +19,7 @@ def _manifest_with_runtime(value: object) -> dict[str, Any]:
 
 class TestManifestRuntimeRemoved(unittest.TestCase):
     def test_loads_when_runtime_absent(self):
-        m = Manifest.from_json_obj({
+        m = ManifestIndex.from_json_obj({
             "bottles": {"dev": {}},
             "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
         })
@@ -32,7 +32,7 @@ class TestManifestRuntimeRemoved(unittest.TestCase):
         for value in ("runsc", "runc", "kata-runtime", "", 42, None):
             with self.subTest(value=value):
                 with self.assertRaises(ManifestError):
-                    Manifest.from_json_obj(_manifest_with_runtime(value))
+                    ManifestIndex.from_json_obj(_manifest_with_runtime(value))
 
 
 if __name__ == "__main__":

tests/unit/test_plan_print_parity.py

@@ -19,19 +19,18 @@ from bot_bottle.backend.docker.bottle_plan import DockerBottlePlan
 from bot_bottle.backend.smolmachines.bottle_plan import SmolmachinesBottlePlan
 from bot_bottle.egress import EgressPlan, EgressRoute
 from bot_bottle.git_gate import GitGatePlan, GitGateUpstream
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import Manifest, ManifestIndex
 
 
-def _manifest() -> Manifest:
-    return Manifest.from_json_obj({
-        "bottles": {"dev": {}},
-        "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
-    })
+_INDEX = ManifestIndex.from_json_obj({
+    "bottles": {"dev": {}},
+    "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
+})
 
 
-def _spec(manifest: Manifest, tmp: str) -> BottleSpec:
+def _spec(index: ManifestIndex, tmp: str) -> BottleSpec:
     return BottleSpec(
-        manifest=manifest,
+        manifest=index,
         agent_name="demo",
         copy_cwd=False,
         user_cwd=tmp,
@@ -92,10 +91,11 @@ def _agent_provision(tmp: str) -> AgentProvisionPlan:
     )
 
 
-def _docker_plan(spec: BottleSpec, tmp: str) -> DockerBottlePlan:
+def _docker_plan(spec: BottleSpec, manifest: Manifest, tmp: str) -> DockerBottlePlan:
     stage = Path(tmp)
     return DockerBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=stage,
         git_gate_plan=_git_gate_plan(tmp),
         egress_plan=_egress_plan(tmp),
@@ -107,10 +107,11 @@ def _docker_plan(spec: BottleSpec, tmp: str) -> DockerBottlePlan:
     )
 
 
-def _smolmachines_plan(spec: BottleSpec, tmp: str) -> SmolmachinesBottlePlan:
+def _smolmachines_plan(spec: BottleSpec, manifest: Manifest, tmp: str) -> SmolmachinesBottlePlan:
     stage = Path(tmp)
     return SmolmachinesBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=stage,
         git_gate_plan=_git_gate_plan(tmp),
         egress_plan=_egress_plan(tmp),
@@ -140,10 +141,10 @@ class TestGitGatePrintParity(unittest.TestCase):
 
     def setUp(self) -> None:
         self._tmp = tempfile.mkdtemp(prefix="plan-print-parity-")
-        manifest = _manifest()
-        spec = _spec(manifest, self._tmp)
-        self._docker_lines = _capture_print(_docker_plan(spec, self._tmp))
-        self._smol_lines = _capture_print(_smolmachines_plan(spec, self._tmp))
+        manifest = _INDEX.load_for_agent("demo")
+        spec = _spec(_INDEX, self._tmp)
+        self._docker_lines = _capture_print(_docker_plan(spec, manifest, self._tmp))
+        self._smol_lines = _capture_print(_smolmachines_plan(spec, manifest, self._tmp))
 
     def _git_gate_lines(self, lines: list[str]) -> list[str]:
         return [ln for ln in lines if "git gate" in ln]
@@ -170,10 +171,10 @@ class TestEgressPrintParity(unittest.TestCase):
 
     def setUp(self) -> None:
         self._tmp = tempfile.mkdtemp(prefix="plan-print-parity-")
-        manifest = _manifest()
-        spec = _spec(manifest, self._tmp)
-        self._docker_lines = _capture_print(_docker_plan(spec, self._tmp))
-        self._smol_lines = _capture_print(_smolmachines_plan(spec, self._tmp))
+        manifest = _INDEX.load_for_agent("demo")
+        spec = _spec(_INDEX, self._tmp)
+        self._docker_lines = _capture_print(_docker_plan(spec, manifest, self._tmp))
+        self._smol_lines = _capture_print(_smolmachines_plan(spec, manifest, self._tmp))
 
     def _egress_section(self, lines: list[str]) -> list[str]:
         """Return lines from the egress label through the last route entry.

tests/unit/test_provision_git.py

@@ -10,7 +10,7 @@ from bot_bottle.git_gate import (
     GIT_GATE_HOSTNAME,
     git_gate_render_gitconfig,
 )
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from tests.fixtures import fixture_minimal, fixture_with_git
 
 
@@ -72,7 +72,7 @@ class TestGitGateGitconfigRender(unittest.TestCase):
     def test_ip_upstream_emits_single_insteadof(self):
         # In the new format the dict key is the repo name, not a host
         # alias, so there is only one insteadOf rule — for the IP URL.
-        m = Manifest.from_json_obj({
+        m = ManifestIndex.from_json_obj({
             "bottles": {"dev": {"git-gate": {"repos": {
                 "bot-bottle": {
                     "url": "ssh://git@100.78.141.42:30009/didericis/bot-bottle.git",

tests/unit/test_smolmachines_provision.py

@@ -33,7 +33,7 @@ from bot_bottle.backend.smolmachines.launch import _bundle_launch_spec
 from bot_bottle.backend.util import AGENT_CA_PATH
 from bot_bottle.egress import EgressPlan, EgressRoute
 from bot_bottle.git_gate import GitGatePlan, GitGateUpstream
-from bot_bottle.manifest import ManifestGitEntry, ManifestKeyConfig, Manifest
+from bot_bottle.manifest import ManifestGitEntry, ManifestKeyConfig, ManifestIndex
 from bot_bottle.supervise import SupervisePlan
 
 
@@ -110,7 +110,7 @@ def _plan(
         bottle_json["git-gate"] = git_gate_json
     if supervise:
         bottle_json["supervise"] = True
-    manifest = Manifest.from_json_obj({
+    index = ManifestIndex.from_json_obj({
         "bottles": {"dev": bottle_json},
         "agents": {
             "demo": {
@@ -120,8 +120,9 @@ def _plan(
             },
         },
     })
+    manifest = index.load_for_agent("demo")
     spec = BottleSpec(
-        manifest=manifest,
+        manifest=index,
         agent_name="demo",
         copy_cwd=copy_cwd,
         user_cwd=user_cwd,
@@ -135,6 +136,7 @@ def _plan(
         )
     return SmolmachinesBottlePlan(
         spec=spec,
+        manifest=manifest,
         stage_dir=stage_dir or Path("/tmp/stage"),
         slug="demo-abc12",
         bundle_subnet="192.168.50.0/24",