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>

scripts/deploy-manifest.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Deployment manifest — sourced by install.sh and sync.sh (Chunk 6).
+# Deployment manifest — sourced by install.sh.
 # All paths: src relative to REPO_ROOT, dest relative to HOME.
 # Format: "src:dest"
 
@@ -21,7 +21,4 @@ DEPLOY_DIRS=(
   "core:.claude/core"
 )
 
-# Skills — merged per-skill into canonical location (parent not wiped, user skills preserved)
-DEPLOY_SKILLS_SRC=".agents/skills"
-
 # Provider skill adapters are declared in providers/*/provider-manifest.sh, not here.