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>

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 ""