chore: remove stale chunk/skills references from vision, scripts, and tests

## Why
The repo moved from a chunk-based delivery model with `.agents/skills/`
as the canonical skill source to a plugin model. Several files retained
references to the old model that were either dead code or misleading
framing.

## Impact
- `tests/test-install.sh`: dead `.agents/skills/` test blocks removed;
  suite now tests only what `install.sh` actually deploys
- `scripts/deploy-manifest.sh`: `DEPLOY_SKILLS_SRC` variable and stale
  `sync.sh (Chunk 6)` comment removed
- `tests/test-git-hooks-install.sh`: fixture stub no longer declares
  the removed `DEPLOY_SKILLS_SRC` variable
- `docs/VISION.md`: chunk delivery framing replaced with plugin model
  language throughout; manual test plan date updated
- `tests/test-instructions-and-docs.sh`: stale test plan date flagged
  as pre-refactor so readers know a re-run is needed

Refs: #15

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

docs/VISION.md

@@ -19,8 +19,8 @@ Designed to start as a personal homelab tool and grow into something shareable w
 
 - Automatic push-based sync to projects
 - Runtime dependency from projects back to this repo
-- Bootstrapping new projects (`init-project.sh` comes in chunk 6)
-- GitHub Copilot support (chunk 7)
+- Bootstrapping new projects (`init-project.sh` — not yet built)
+- GitHub Copilot support (not yet built)
 
 ## Current architecture
 
@@ -30,9 +30,9 @@ See `docs/spec/architecture.md` for the deployed directory structure, content de
 
 V1 is "ready to develop" — not a finished product. It means this repo is structured, Claude Code is wired up to it, and there is enough initial content to start building incrementally.
 
-**V1 = Chunk 1 complete — ✅ done.**
+**V1 = core install pipeline complete — ✅ done.**
 
-Everything from chunk 2 onward is content and tooling built on top of that foundation.
+All content and tooling is built incrementally on top of that foundation via plugins.
 
 ## Long-term: Management Application
 
@@ -56,7 +56,7 @@ Browse, edit, and configure AI development config through a proper product UI.
 - Hosting: self-hosted first, cloud-hosted option later
 - Users: solo-first, multi-user-ready data model from day one
 
-**Start trigger:** after Chunk 6 of this repo (`sync.sh` + `init-project.sh`). Full content model and sync tooling must be stable before building a UI over them.
+**Start trigger:** when the plugin content model and sync tooling are stable. Full content model must be stable before building a UI over it.
 
 **Mobile/desktop (Phase 3):** React → React Native for mobile; Tauri to wrap the web app for desktop.