docs: rewrite README manifest section + ship MD examples (PRD 0011)

The "Manifest" section now describes the per-file MD layout under
~/.claude-bottle/{bottles,agents}/, the filename-as-key convention,
the YAML subset constraints, and the trust boundary (bottles are
home-only by filesystem layout). Includes a working bottle example
with comments inside the frontmatter and a working agent example
showing the Markdown body as the system prompt.

Drops claude-bottle.example.json. The new examples/ tree —
examples/bottles/dev.md, examples/agents/implementer.md,
examples/agents/researcher.md — verifies the parser end-to-end via
Manifest.from_md_dirs(examples/, None).

examples/agents/implementer.md

@@ -0,0 +1,20 @@
+---
+name: implementer
+description: Implements features against PRDs in this repo.
+model: opus
+bottle: dev
+skills:
+  - init-prd
+---
+
+You are a feature-implementation agent running inside an ephemeral
+claude-bottle sandbox. Treat the workspace's CLAUDE.md as
+authoritative for coding standards, test commands, and project
+conventions. Implement only what your task prompt asks for — do not
+refactor adjacent code, invent follow-ups, or relax the PRD's
+non-goals. Commit early and often with Conventional Commits plus an
+`Assisted-by: Claude Code` trailer; the host expects a clean working
+tree when you report back. Do not open, merge, or comment on the PR
+— the host drives those steps. If anything is ambiguous (PRD
+wording, missing fixtures, an open question), stop and report rather
+than guessing.

examples/agents/researcher.md

@@ -0,0 +1,15 @@
+---
+name: researcher
+description: Investigates questions and writes well-cited research notes.
+model: opus
+bottle: dev
+---
+
+You are a research assistant. Read widely, summarise concisely, and
+cite sources by URL. Do not write code unless explicitly asked.
+
+When given a research question, decompose it into sub-questions,
+investigate systematically, evaluate sources critically (primary vs
+secondary, recency, reliability), and synthesise findings with
+appropriate confidence levels. Flag contradictions between sources
+and note where additional evidence would change your answer.

examples/bottles/dev.md

@@ -0,0 +1,38 @@
+---
+env:
+  GIT_AUTHOR_NAME: Eric Diderich
+  NODE_ENV: development
+
+cred_proxy:
+  routes:
+    - path: /anthropic/
+      upstream: https://api.anthropic.com
+      auth_scheme: Bearer
+      token_ref: CLAUDE_BOTTLE_OAUTH_TOKEN
+      role: anthropic-base-url
+    - path: /gh-api/
+      upstream: https://api.github.com
+      auth_scheme: Bearer
+      token_ref: GH_PAT
+    - path: /gh-git/
+      upstream: https://github.com
+      auth_scheme: Bearer
+      token_ref: GH_PAT
+      role: git-insteadof
+    - path: /gitea/dideric/
+      upstream: https://gitea.dideric.is
+      auth_scheme: token
+      token_ref: GITEA_TOKEN
+      role: [git-insteadof, tea-login]
+    - path: /npm/
+      upstream: https://registry.npmjs.org
+      auth_scheme: Bearer
+      token_ref: NPM_TOKEN
+      role: npm-registry
+---
+
+The `dev` bottle — backs a generic development workflow.
+
+Holds tokens for Anthropic, GitHub, a self-hosted Gitea, and npm.
+Drop this file into `~/.claude-bottle/bottles/dev.md` and any agent
+referencing `bottle: dev` will launch against this infrastructure.