chore: remove journal and project-local init-entry skill

Drop docs/JOURNAL.md and .claude/skills/init-entry/, and update
CLAUDE.md, docs/INDEX.md, and claude-bottle.example.json so nothing
points at them anymore.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

claude-bottle.example.json

@@ -44,13 +44,13 @@
   "agents": {
     "researcher": {
       "bottle": "default",
-      "skills": ["init-entry"],
+      "skills": [],
       "prompt": "You are a research assistant. Read widely, summarise concisely, and cite sources by URL. Do not write code unless explicitly asked."
     },
 
     "gitea-helper": {
       "bottle": "gitea-dev",
-      "skills": ["init-entry", "init-prd"],
+      "skills": ["init-prd"],
       "prompt": "You help maintain Gitea-hosted projects. Prefer small, focused commits. Follow Conventional Commits. Run tests before pushing."
     },