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)
+- Bootstrapping new projects (`init-project.sh` — not yet built)
-- GitHub Copilot support (chunk 7)
+- 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.
 

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.

tests/test-git-hooks-install.sh

@@ -32,7 +32,6 @@ cat > "$TEMP_REPO/scripts/deploy-manifest.sh" << 'EOF'
 DEPLOY_FILES=()
 DEPLOY_EXECUTABLES=()
 DEPLOY_DIRS=()
-DEPLOY_SKILLS_SRC=".agents/skills"
 EOF
 
 # Copy the real install.sh and git-hooks into the temp repo

tests/test-install.sh

@@ -59,59 +59,6 @@ else
     fail "\$HOME/.agents/AGENTS.md — missing or differs from source"
 fi
 
-if [[ -d "$REPO_ROOT/.agents/skills" ]]; then
-  echo ""
-  echo "--- skills deployed to ~/.agents/skills/ ---"
-  while IFS= read -r -d '' src_skill; do
-      skill_name="$(basename "$src_skill")"
-      dest_skill="$TEMP_HOME/.agents/skills/$skill_name"
-      if [[ -d "$dest_skill" ]]; then
-          pass "$skill_name deployed to ~/.agents/skills/"
-      else
-          fail "$skill_name missing from ~/.agents/skills/"
-      fi
-  done < <(find "$REPO_ROOT/.agents/skills" -mindepth 1 -maxdepth 1 -type d -print0)
-
-  echo ""
-  echo "--- skill files match source ---"
-  while IFS= read -r -d '' src; do
-      rel="${src#"$REPO_ROOT/.agents/skills/"}"
-      dest="$TEMP_HOME/.agents/skills/$rel"
-      if diff -q "$src" "$dest" > /dev/null 2>&1; then
-          pass "skills/$rel matches source"
-      else
-          fail "skills/$rel — missing or differs from source"
-      fi
-  done < <(find "$REPO_ROOT/.agents/skills" -type f -print0)
-
-  echo ""
-  echo "--- skills correctly replaced on second install (no double-nesting) ---"
-  first_skill="$(find "$REPO_ROOT/.agents/skills" -mindepth 1 -maxdepth 1 -type d | head -1)"
-  if [[ -n "$first_skill" ]]; then
-      skill_name="$(basename "$first_skill")"
-      nested="$TEMP_HOME/.agents/skills/$skill_name/$skill_name"
-      if [[ -d "$nested" ]]; then
-          fail "$skill_name/$skill_name exists — skill was nested instead of replaced"
-      else
-          pass "$skill_name not double-nested after second install"
-      fi
-  fi
-fi
-
-echo ""
-echo "--- user skills preserved after install (merge, not wipe) ---"
-TEMP_HOME2="$(mktemp -d)"
-trap 'rm -rf "$TEMP_HOME2"' EXIT
-# Pre-create a user skill not in the source
-mkdir -p "$TEMP_HOME2/.agents/skills/my-custom-skill"
-echo "custom" > "$TEMP_HOME2/.agents/skills/my-custom-skill/SKILL.md"
-HOME="$TEMP_HOME2" bash "$REPO_ROOT/scripts/install.sh" > /dev/null
-if [[ -f "$TEMP_HOME2/.agents/skills/my-custom-skill/SKILL.md" ]]; then
-    pass "pre-existing user skill preserved after install"
-else
-    fail "pre-existing user skill was wiped by install"
-fi
-
 echo ""
 echo "--- idempotency: second run state is correct ---"
 if HOME="$TEMP_HOME" bash "$REPO_ROOT/scripts/install.sh" > /dev/null 2>&1; then
@@ -120,30 +67,6 @@ else
     fail "second run failed"
 fi
 
-if [[ -d "$REPO_ROOT/.agents/skills" ]]; then
-  # skill files still match source after second run
-  while IFS= read -r -d '' src; do
-      rel="${src#"$REPO_ROOT/.agents/skills/"}"
-      dest="$TEMP_HOME/.agents/skills/$rel"
-      if diff -q "$src" "$dest" > /dev/null 2>&1; then
-          pass "idempotent: skills/$rel correct after second install"
-      else
-          fail "idempotent: skills/$rel corrupted after second install"
-      fi
-  done < <(find "$REPO_ROOT/.agents/skills" -type f -print0)
-
-  # no double-nesting after second run
-  while IFS= read -r -d '' skill_dir; do
-      skill_name="$(basename "$skill_dir")"
-      nested="$TEMP_HOME/.agents/skills/$skill_name/$skill_name"
-      if [[ -d "$nested" ]]; then
-          fail "idempotent: $skill_name double-nested after second install"
-      else
-          pass "idempotent: $skill_name not double-nested after second install"
-      fi
-  done < <(find "$REPO_ROOT/.agents/skills" -mindepth 1 -maxdepth 1 -type d -print0)
-fi
-
 # AGENTS.md still correct after second run
 if diff -q "$REPO_ROOT/core/AGENTS.md" "$TEMP_HOME/.agents/AGENTS.md" > /dev/null 2>&1; then
     pass "idempotent: ~/.agents/AGENTS.md correct after second install"

tests/test-instructions-and-docs.sh

@@ -284,7 +284,7 @@ echo "────────────────────────
 echo "MANUAL TEST PLAN (run in a fresh Claude session)"
 echo "─────────────────────────────────────────────────────"
 echo ""
-echo "Results last run: 2026-05-17 (multiple rounds)"
+echo "Results last run: 2026-06-28 (pre-plugin-refactor; re-run needed)"
 echo "  PASS: 1, 2, 3, 5, 6, 7, 8, 9"
 echo "  INCONCLUSIVE: 4 (no remote configured in test environment)"
 echo ""