@jenga-ai/agent 3.5.0 → 4.0.0

package/scripts/verify-legacy-seed-reconcile.sh

@@ -83,8 +83,8 @@ make_pkg() {
   cat > "$dir/package.json" <<'JSON'
 { "name": "@jenga-ai/agent", "version": "3.0.0", "type": "module" }
 JSON
-  mkdir -p "$dir/skills/do" "$dir/agents"
-  printf '# do skill (still shipped)\n' > "$dir/skills/do/SKILL.md"
+  mkdir -p "$dir/skills/j-do" "$dir/agents"
+  printf '# do skill (still shipped)\n' > "$dir/skills/j-do/SKILL.md"
   printf '# developer agent (still shipped)\n' > "$dir/agents/developer.md"
 }
 
@@ -116,7 +116,7 @@ PKG="$FIXTURE/pkg"
 make_pkg "$PKG"
 write_legacy_paths "$PKG" \
   "agents/developer.md" \
-  "skills/do/SKILL.md" \
+  "skills/j-do/SKILL.md" \
   "skills/j-legacy-twin/SKILL.md" \
   "../OUTSIDE-THE-FIXTURE.txt" \
   "skills/trap/LINK.md"
@@ -146,7 +146,7 @@ assert_dir "$CONSUMER_A/.agents/skills/j-legacy-twin" \
   "directory survives because it still holds a consumer file (.agents)"
 assert_grep "seeded from known-shipped legacy paths" "$FIXTURE/a-install.log" \
   "install log attributes the cleanup to legacy-path seeding"
-assert_file "$CONSUMER_A/.agents/skills/do/SKILL.md" \
+assert_file "$CONSUMER_A/.agents/skills/j-do/SKILL.md" \
   "currently-shipped skill untouched"
 assert_file "$CONSUMER_A/.agents/agents/developer.md" \
   "currently-shipped agent file untouched"
@@ -158,7 +158,7 @@ import json, sys
 paths = json.load(open(sys.argv[1]))["paths"]
 assert "skills/j-legacy-twin/SKILL.md" not in paths, "deleted orphan must not be in the fresh manifest"
 assert "skills/j-legacy-twin/my-notes.md" not in paths, "consumer file must never be in the manifest"
-assert "skills/do/SKILL.md" in paths and "agents/developer.md" in paths, "current package paths must be present"
+assert "skills/j-do/SKILL.md" in paths and "agents/developer.md" in paths, "current package paths must be present"
 PYEOF
 if [ $? -eq 0 ]; then pass "fresh manifest describes only what is actually on disk post-cleanup"; else fail "fresh manifest is inaccurate"; fi
 
@@ -174,13 +174,13 @@ assert_nogrep_re "[1-9][0-9]* stale file" "$FIXTURE/b-install.log" \
   "first-ever install deletes nothing despite a non-empty legacy path list"
 assert_grep "no previous install manifest" "$FIXTURE/b-install.log" \
   "first-ever install reports plain additive-only, not a seeded outcome"
-assert_file "$CONSUMER_B/.agents/skills/do/SKILL.md" \
+assert_file "$CONSUMER_B/.agents/skills/j-do/SKILL.md" \
   "first-ever install still copies current package files"
 
 # ═══ Scenario C — a legacy path still currently shipped is never touched ═════
-# (Implicitly exercised by Scenario A's "do"/"developer.md" already surviving, but
+# (Implicitly exercised by Scenario A's "j-do"/"developer.md" already surviving, but
 # asserted here as its own named check for clarity.)
-assert_file "$CONSUMER_A/.claude/skills/do/SKILL.md" \
+assert_file "$CONSUMER_A/.claude/skills/j-do/SKILL.md" \
   "a legacy-listed path that is STILL shipped survives untouched (not stale)"
 
 # ═══ Scenario D — a legacy path absent from disk is never phantom-seeded ═════
@@ -219,7 +219,7 @@ PKG_F1="$FIXTURE/pkg-f1"
 make_pkg "$PKG_F1"
 mkdir -p "$PKG_F1/skills/renamed-old"
 printf '# renamed-old — removed in the next version\n' > "$PKG_F1/skills/renamed-old/SKILL.md"
-write_legacy_paths "$PKG_F1" "agents/developer.md" "skills/do/SKILL.md"
+write_legacy_paths "$PKG_F1" "agents/developer.md" "skills/j-do/SKILL.md"
 
 PKG_F2="$FIXTURE/pkg-f2"
 make_pkg "$PKG_F2"
@@ -228,7 +228,7 @@ import json
 p = '$PKG_F2/package.json'
 d = json.load(open(p)); d['version'] = '3.0.1'; json.dump(d, open(p, 'w'))
 "
-write_legacy_paths "$PKG_F2" "agents/developer.md" "skills/do/SKILL.md" "skills/renamed-old/SKILL.md"
+write_legacy_paths "$PKG_F2" "agents/developer.md" "skills/j-do/SKILL.md" "skills/renamed-old/SKILL.md"
 
 CONSUMER_F="$FIXTURE/consumer-f"
 mkdir -p "$CONSUMER_F"

package/scripts/verify-postinstall-reconcile.sh

@@ -90,7 +90,7 @@ echo "  fixture: $FIXTURE"
 # ── package v1.0.0 ───────────────────────────────────────────────────────────
 PKG1="$FIXTURE/pkg-v1"
 make_pkg "$PKG1" "1.0.0"
-add_skill "$PKG1" "do"           "# do — stable across both versions"
+add_skill "$PKG1" "j-do"         "# j-do — stable across both versions"
 add_skill "$PKG1" "renamed-old"  "# renamed-old — becomes renamed-new in v2"
 add_skill "$PKG1" "j-legacy-twin" "# j-legacy-twin — excluded in v2 (E50_S06 style)"
 printf '# developer agent v1\n' > "$PKG1/agents/developer.md"
@@ -98,7 +98,7 @@ printf '# developer agent v1\n' > "$PKG1/agents/developer.md"
 # ── package v2.0.0 ───────────────────────────────────────────────────────────
 PKG2="$FIXTURE/pkg-v2"
 make_pkg "$PKG2" "2.0.0"
-add_skill "$PKG2" "do"           "# do — stable across both versions"   # byte-identical
+add_skill "$PKG2" "j-do"         "# j-do — stable across both versions"   # byte-identical
 add_skill "$PKG2" "renamed-new"  "# renamed-new — replaces renamed-old"
 # j-legacy-twin intentionally absent (excluded), renamed-old intentionally absent
 printf '# developer agent v2 (changed)\n' > "$PKG2/agents/developer.md"
@@ -136,7 +136,7 @@ assert_file "$CONSUMER/.claude/.jenga-postinstall-manifest.json" \
   "manifest written to .claude on first install"
 assert_nogrep "preexisting/JUNK.md" "$CONSUMER/.agents/.jenga-postinstall-manifest.json" \
   "consumer file is NOT recorded in the manifest"
-assert_grep "skills/do/SKILL.md" "$CONSUMER/.agents/.jenga-postinstall-manifest.json" \
+assert_grep "skills/j-do/SKILL.md" "$CONSUMER/.agents/.jenga-postinstall-manifest.json" \
   "manifest records mirrored package paths"
 
 # ═══ Scenario B — upgrade with renames / removals / exclusions ════════════════
@@ -153,7 +153,7 @@ done
 
 # Record identity of a file common to both versions, to prove it is not needlessly
 # deleted and recopied (mirror() should classify it as `skipped`).
-DO_BEFORE="$(ls -li "$CONSUMER/.agents/skills/do/SKILL.md" | awk '{print $1, $6, $7, $8}')"
+DO_BEFORE="$(ls -li "$CONSUMER/.agents/skills/j-do/SKILL.md" | awk '{print $1, $6, $7, $8}')"
 
 run_install "$PKG2" "$CONSUMER" "$FIXTURE/install-v2.log"
 
@@ -196,7 +196,7 @@ assert_file "$CONSUMER/.claude/skills/renamed-new/SKILL.md" \
   "renamed-to skill installed (.claude)"
 
 # 5. Unchanged common file was neither deleted nor recopied.
-DO_AFTER="$(ls -li "$CONSUMER/.agents/skills/do/SKILL.md" | awk '{print $1, $6, $7, $8}')"
+DO_AFTER="$(ls -li "$CONSUMER/.agents/skills/j-do/SKILL.md" | awk '{print $1, $6, $7, $8}')"
 if [ "$DO_BEFORE" = "$DO_AFTER" ]; then
   pass "file common to both versions untouched (same inode+mtime)"
 else
@@ -375,9 +375,9 @@ mkdir -p "$CONSUMER_M"
 run_install "$PKG1" "$CONSUMER_M" "$FIXTURE/missing-v1.log"
 run_install "$PKG2M" "$CONSUMER_M" "$FIXTURE/missing-v2.log"
 
-assert_file "$CONSUMER_M/.agents/skills/do/SKILL.md" \
+assert_file "$CONSUMER_M/.agents/skills/j-do/SKILL.md" \
   "missing copySet entry does not wipe the mirrored subtree (.agents)"
-assert_file "$CONSUMER_M/.claude/skills/do/SKILL.md" \
+assert_file "$CONSUMER_M/.claude/skills/j-do/SKILL.md" \
   "missing copySet entry does not wipe the mirrored subtree (.claude)"
 assert_grep "Upgrade cleanup skipped" "$FIXTURE/missing-v2.log" \
   "packaging regression reported, cleanup skipped"

package/scripts/write-context-digest.sh

@@ -32,7 +32,7 @@
 #   <producer> | write-context-digest.sh --agent <agent> --session-id <id> --task-id <id>
 #
 # If neither --content nor --content-file is given, digest content is read
-# from stdin (mirrors skills/uncharted/scripts/import-source.sh's snippet
+# from stdin (mirrors skills/j-uncharted/scripts/import-source.sh's snippet
 # convention).
 #
 # Options:

package/skills/j-brainstorm/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.brainstorm
-description: Polyfill alias of the brainstorm skill under a collision-safe directory name. Identical behavior to /brainstorm — Engage the scrum-master agent in a focused planning session to define, refine, or challenge features, improvements, tasks, stories, and epics. The agent asks probing questions, challenges assumptions, and helps shape ideas into actionable backlog items. Use when the bare /brainstorm form is shadowed by another tool's own built-in command of the same name.
+description: Engage the scrum-master agent in a focused planning session to define, refine, or challenge features, improvements, tasks, stories, and epics. The agent asks probing questions, challenges assumptions, and helps shape ideas into actionable backlog items.
 keywords:
   - brainstorm
   - plan
@@ -8,7 +8,6 @@ keywords:
   - feature planning
   - requirements
   - j-brainstorm
-  - polyfill
 examples:
   - "let's brainstorm ideas for X"
   - "I need to plan a new feature"
@@ -19,9 +18,9 @@ metadata:
 
 # Brainstorm — Collaborative Planning with the Scrum Master
 
-This skill is a literal-directory-name duplicate of `skills/brainstorm/`. It exists so that `/j-brainstorm` (and `j.j-brainstorm`) give a guaranteed-unshadowed way to reach the same flow as `/brainstorm`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/brainstorm` alias (Claude Code's native skill resolution is a literal-string, directory-name-based match — see `docs/skill-authoring.md`'s "Invocation Convention").
+`skills/j-brainstorm/` is the **canonical, hand-edited** directory for this skill, per CLAUDE.md's "The Canonical Naming Contract" (the `E50` reopening of 2026-09-09, which promoted `skills/j-brainstorm/` from generated twin to sole canonical form). The `j-` prefix is there for collision safety — a real directory under a distinct name, so a host tool shipping its own same-named built-in command cannot shadow it (Claude Code's native skill resolution is a literal-string, directory-name-based match; see `docs/skill-authoring.md`'s "Invocation Convention").
 
-This file is generated/synced by `scripts/generate-j-alias.sh brainstorm` from `skills/brainstorm/SKILL.md` — do not hand-edit it; re-run the generator instead to pick up source changes.
+> ⚠️ **`scripts/generate-j-alias.sh` was retired by `E50_S14` and no longer exists — there is nothing to run.** This file was previously generated from a bare `skills/brainstorm/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## Instructions
 

package/skills/j-btw/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.btw
-description: Polyfill alias of the btw skill under a collision-safe directory name. Identical behavior to /btw — Capture a new mission (feature, change, or addition) and fit it into the project's Epic/Story structure, then choose to implement now or defer. Use when the bare /btw form is shadowed by another tool's own built-in command of the same name.
+description: Capture a new mission (feature, change, or addition) and fit it into the project's Epic/Story structure, then choose to implement now or defer.
 keywords:
   - btw
   - capture
@@ -8,7 +8,6 @@ keywords:
   - new idea
   - side task
   - j-btw
-  - polyfill
 examples:
   - "btw I also need to add X"
   - "capture this as a new task"
@@ -19,9 +18,9 @@ metadata:
 
 # BTW — Capture a Mission
 
-This skill is a literal-directory-name duplicate of `skills/btw/`. It exists so that `/j-btw` (and `j.j-btw`) give a guaranteed-unshadowed way to reach the same flow as `/btw`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/btw` alias (Claude Code's native skill resolution is a literal-string, directory-name-based match — see `docs/skill-authoring.md`'s "Invocation Convention").
+`skills/j-btw/` is the **canonical, hand-edited** directory for this skill, per CLAUDE.md's "The Canonical Naming Contract" (the `E50` reopening of 2026-09-09, which promoted `skills/j-btw/` from generated twin to sole canonical form). The `j-` prefix is there for collision safety — a real directory under a distinct name, so a host tool shipping its own same-named built-in command cannot shadow it (Claude Code's native skill resolution is a literal-string, directory-name-based match; see `docs/skill-authoring.md`'s "Invocation Convention").
 
-This file is generated/synced by `scripts/generate-j-alias.sh btw` from `skills/btw/SKILL.md` — do not hand-edit it; re-run the generator instead to pick up source changes.
+> ⚠️ **`scripts/generate-j-alias.sh` was retired by `E50_S14` and no longer exists — there is nothing to run.** This file was previously generated from a bare `skills/btw/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## Instructions
 

package/skills/j-clearify/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.clearify
-description: Polyfill alias of the clearify skill under a collision-safe directory name. Identical behavior to /clearify — Clarifies ambiguous, dense, or under-specified prompts and conversation on request — inspects an attached prompt or falls back to the current conversation and surfaces plain-language clarifications with examples. Use when the bare /clearify form is shadowed by another tool's own built-in command of the same name.
+description: Clarifies ambiguous, dense, or under-specified prompts and conversation on request — inspects an attached prompt or falls back to the current conversation and surfaces plain-language clarifications with examples.
 keywords:
   - clarify this
   - clarify
@@ -10,7 +10,6 @@ keywords:
   - explain that again
   - can you simplify
   - j-clearify
-  - polyfill
 examples:
   - "clarify this"
   - "clearify the last message"
@@ -22,11 +21,11 @@ alias: wtf
 
 # Clearify — Ambiguity Clarification
 
-This skill is a literal-directory-name duplicate of `skills/clearify/`. It exists so that `/j-clearify` (and `j.j-clearify`) give a guaranteed-unshadowed way to reach the same flow as `/clearify`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/clearify` alias (Claude Code's native skill resolution is a literal-string, directory-name-based match — see `docs/skill-authoring.md`'s "Invocation Convention").
+`skills/j-clearify/` is the **canonical, hand-edited** directory for this skill, per CLAUDE.md's "The Canonical Naming Contract" (the `E50` reopening of 2026-09-09, which promoted `skills/j-clearify/` from generated twin to sole canonical form). The `j-` prefix is there for collision safety — a real directory under a distinct name, so a host tool shipping its own same-named built-in command cannot shadow it (Claude Code's native skill resolution is a literal-string, directory-name-based match; see `docs/skill-authoring.md`'s "Invocation Convention").
 
-This file is generated/synced by `scripts/generate-j-alias.sh clearify` from `skills/clearify/SKILL.md` — do not hand-edit it; re-run the generator instead to pick up source changes.
+> ⚠️ **`scripts/generate-j-alias.sh` was retired by `E50_S14` and no longer exists — there is nothing to run.** This file was previously generated from a bare `skills/clearify/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
-> **Note on the `alias: wtf` frontmatter field:** this repo has no runtime mechanism that reads an `alias` key to route slash commands — no existing `SKILL.md` implements one, and `project/configs/workflow.json` has no alias registry. The field here documents the intended relationship only. `/wtf` is made invocable as a working alias by the companion skill folder at `skills/wtf/SKILL.md`, which delegates to these same instructions.
+> **Note on the `alias: wtf` frontmatter field:** this repo has no runtime mechanism that reads an `alias` key to route slash commands — no existing `SKILL.md` implements one, and `project/configs/workflow.json` has no alias registry. The field here documents the intended relationship only. `/wtf` is made invocable as a working alias by the companion skill folder at `skills/j-wtf/SKILL.md`, which delegates to these same instructions.
 
 ## Instructions
 
@@ -56,4 +55,4 @@ This file is generated/synced by `scripts/generate-j-alias.sh clearify` from `sk
 ## Examples
 - `/clearify` — Clarify the most recent user message / relevant conversation context
 - `/clearify <pasted text>` — Clarify the attached text directly
-- `/wtf` — Alias for `/clearify`, invoked via the companion skill in `skills/wtf/`
+- `/wtf` — Alias for `/clearify`, invoked via the companion skill in `skills/j-wtf/`

package/skills/j-close-story/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.close-story
-description: Polyfill alias of the close-story skill under a collision-safe directory name. Identical behavior to /close-story — Close a story by verifying all tasks are in terminal state, extracting actual diff stats per task, computing scope divergence flags, and writing closure metadata to task frontmatter. Use when the bare /close-story form is shadowed by another tool's own built-in command of the same name.
+description: Close a story by verifying all tasks are in terminal state, extracting actual diff stats per task, computing scope divergence flags, and writing closure metadata to task frontmatter.
 keywords:
   - close story
   - close
@@ -8,7 +8,6 @@ keywords:
   - complete story
   - story done
   - j-close-story
-  - polyfill
 examples:
   - "close story E17_S06"
   - "/close-story E32_S06"
@@ -18,9 +17,9 @@ examples:
 
 # close-story — Close a Story
 
-This skill is a literal-directory-name duplicate of `skills/close-story/`. It exists so that `/j-close-story` (and `j.j-close-story`) give a guaranteed-unshadowed way to reach the same flow as `/close-story`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/close-story` alias (Claude Code's native skill resolution is a literal-string, directory-name-based match — see `docs/skill-authoring.md`'s "Invocation Convention").
+`skills/j-close-story/` is the **canonical, hand-edited** directory for this skill, per CLAUDE.md's "The Canonical Naming Contract" (the `E50` reopening of 2026-09-09, which promoted `skills/j-close-story/` from generated twin to sole canonical form). The `j-` prefix is there for collision safety — a real directory under a distinct name, so a host tool shipping its own same-named built-in command cannot shadow it (Claude Code's native skill resolution is a literal-string, directory-name-based match; see `docs/skill-authoring.md`'s "Invocation Convention").
 
-This file is generated/synced by `scripts/generate-j-alias.sh close-story` from `skills/close-story/SKILL.md` — do not hand-edit it; re-run the generator instead to pick up source changes.
+> ⚠️ **`scripts/generate-j-alias.sh` was retired by `E50_S14` and no longer exists — there is nothing to run.** This file was previously generated from a bare `skills/close-story/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## Purpose
 
@@ -45,7 +44,7 @@ This file is generated/synced by `scripts/generate-j-alias.sh close-story` from
 Run the guard script:
 
 ```bash
-bash skills/j-close-story/scripts/check-story-closeable.sh <story-id>
+bash "$([ -f skills/j-close-story/scripts/check-story-closeable.sh ] && echo skills/j-close-story/scripts/check-story-closeable.sh || echo node_modules/@jenga-ai/agent/skills/j-close-story/scripts/check-story-closeable.sh)" <story-id>
 ```
 
 - If it exits with code 0 and prints `CLOSEABLE`, continue.
@@ -72,7 +71,7 @@ For **each task ID** listed in the story's `tasks:` frontmatter array:
 
 3. **Run per-task diff stat extraction:**
    ```bash
-   bash skills/j-close-story/scripts/extract-task-diff-stats.sh <task-id>
+   bash "$([ -f skills/j-close-story/scripts/extract-task-diff-stats.sh ] && echo skills/j-close-story/scripts/extract-task-diff-stats.sh || echo node_modules/@jenga-ai/agent/skills/j-close-story/scripts/extract-task-diff-stats.sh)" <task-id>
    ```
    The script outputs:
    ```
@@ -83,11 +82,11 @@ For **each task ID** listed in the story's `tasks:` frontmatter array:
 
 4. **Write stats to task frontmatter:**
    ```bash
-   bash skills/j-close-story/scripts/update-task-frontmatter.sh \
+   bash "$([ -f skills/j-close-story/scripts/update-task-frontmatter.sh ] && echo skills/j-close-story/scripts/update-task-frontmatter.sh || echo node_modules/@jenga-ai/agent/skills/j-close-story/scripts/update-task-frontmatter.sh)" \
      "project/board/tasks/<task-id>_*.md" \
      actual_files_changed <N>
 
-   bash skills/j-close-story/scripts/update-task-frontmatter.sh \
+   bash "$([ -f skills/j-close-story/scripts/update-task-frontmatter.sh ] && echo skills/j-close-story/scripts/update-task-frontmatter.sh || echo node_modules/@jenga-ai/agent/skills/j-close-story/scripts/update-task-frontmatter.sh)" \
      "project/board/tasks/<task-id>_*.md" \
      actual_lines_delta <N>
    ```
@@ -104,13 +103,13 @@ For **each task ID** listed in the story's `tasks:` frontmatter array:
 
    Run the divergence computation:
    ```bash
-   DIVERGENCE_FLAG=$(bash skills/j-close-story/scripts/compute-scope-divergence.sh \
+   DIVERGENCE_FLAG=$(bash "$([ -f skills/j-close-story/scripts/compute-scope-divergence.sh ] && echo skills/j-close-story/scripts/compute-scope-divergence.sh || echo node_modules/@jenga-ai/agent/skills/j-close-story/scripts/compute-scope-divergence.sh)" \
      "<execution_scope>" <actual_files_changed> <actual_lines_delta>)
    ```
 
    Write the result to task frontmatter:
    ```bash
-   bash skills/j-close-story/scripts/update-task-frontmatter.sh \
+   bash "$([ -f skills/j-close-story/scripts/update-task-frontmatter.sh ] && echo skills/j-close-story/scripts/update-task-frontmatter.sh || echo node_modules/@jenga-ai/agent/skills/j-close-story/scripts/update-task-frontmatter.sh)" \
      "project/board/tasks/<task-id>_*.md" \
      scope_divergence_flag "$DIVERGENCE_FLAG"
    ```
@@ -127,7 +126,7 @@ For **each task ID** listed in the story's `tasks:` frontmatter array:
    frontmatter writes and divergence computation above, check whether this
    task's own work is permanently excluded from the public mirror:
    ```bash
-   bash skills/j-close-story/scripts/check-privatized.sh <task-id> "project/board/tasks/<task-id>_*.md"
+   bash "$([ -f skills/j-close-story/scripts/check-privatized.sh ] && echo skills/j-close-story/scripts/check-privatized.sh || echo node_modules/@jenga-ai/agent/skills/j-close-story/scripts/check-privatized.sh)" <task-id> "project/board/tasks/<task-id>_*.md"
    ```
    This is a **static** check (per `$([ -f templates/SCRUM_BOARD_SCHEMA.md ] && echo templates/SCRUM_BOARD_SCHEMA.md || echo node_modules/@jenga-ai/agent/templates/SCRUM_BOARD_SCHEMA.md)`'s "Static
    vs. Reactive Status Setting" section) — it derives the task's touched-file
@@ -177,7 +176,7 @@ against the story's own direct commits (E51_S03_T03) **before** deciding the
 story's terminal status:
 
 ```bash
-bash skills/j-close-story/scripts/check-privatized.sh <story-id> "project/board/stories/<story-id>_*.md"
+bash "$([ -f skills/j-close-story/scripts/check-privatized.sh ] && echo skills/j-close-story/scripts/check-privatized.sh || echo node_modules/@jenga-ai/agent/skills/j-close-story/scripts/check-privatized.sh)" <story-id> "project/board/stories/<story-id>_*.md"
 ```
 
 Passing the story id (`E##_S##`) rather than a task id makes the script's

package/skills/j-close-story/scripts/check-privatized.sh

@@ -5,8 +5,8 @@
 # Static (run-independent) `.publicignore` membership check for a single
 # board ticket, invoked by /close-story at both task granularity (Step 2's
 # per-task loop) and story granularity (Step 4's finalization), per
-# E51_S03_T03. Unlike `Merged` (skills/self-sync/scripts/mark-merged.sh) and
-# `Publicized` (skills/mirror-public/scripts/mark-publicized.sh, E51_S03_T02),
+# E51_S03_T03. Unlike `Merged` (skills/j-self-sync/scripts/mark-merged.sh) and
+# `Publicized` (skills/j-mirror-public/scripts/mark-publicized.sh, E51_S03_T02),
 # which both react to a specific run's file diff, `Privatized` has NO
 # dependency on any run ever having occurred -- it is a pure blocklist
 # membership test against the ticket's own derived touched-file list, per
@@ -25,7 +25,7 @@
 #                       write target.
 #
 # Touched-file derivation -- IDENTICAL technique to
-# skills/self-sync/scripts/mark-merged.sh (reused, not reinvented, per this
+# skills/j-self-sync/scripts/mark-merged.sh (reused, not reinvented, per this
 # task's own description):
 #   1. git log --all --no-merges --extended-regexp \
 #        --grep="<id>([^0-9_]|$)" --pretty=format:'%H'
@@ -41,7 +41,7 @@
 #   4. Zero matched commits -> nothing to check -> UNCHANGED (not an error).
 #
 # .publicignore matching -- ported (not sourced) from
-# skills/mirror-public/scripts/mirror.sh's `_publicignore_rule_for` helper:
+# skills/j-mirror-public/scripts/mirror.sh's `_publicignore_rule_for` helper:
 # directory-prefix match for trailing-"/" lines, glob match against the full
 # relative path and the basename for everything else, skipping comments,
 # blank lines, and "+"-prefixed include lines (which never block anything).

package/skills/j-close-story/scripts/check-story-closeable.sh

@@ -21,11 +21,18 @@ usage() {
   exit 1
 }
 
-# Locate the project root relative to this script's location.
-# Script lives at: skills/j-close-story/scripts/check-story-closeable.sh
-# Project root is three levels up (skills/ → repo root).
+# Locate the project root via git, not a fixed relative climb — this script
+# is deployed both at its source location (skills/j-close-story/scripts/)
+# and mirrored to .claude/skills/j-close-story/scripts/, and a fixed "three
+# levels up" climb lands in the wrong place from the mirror. Same approach as
+# this directory's siblings: check-privatized.sh:138 and
+# compute-scope-divergence.sh:54.
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-PROJECT_ROOT="$(cd "$SCRIPT_DIR/../../.." && pwd)"
+PROJECT_ROOT="$(git -C "$SCRIPT_DIR" rev-parse --show-toplevel 2>/dev/null || true)"
+if [[ -z "$PROJECT_ROOT" ]]; then
+  echo "ERROR: could not locate project root (git rev-parse --show-toplevel failed from $SCRIPT_DIR)" >&2
+  exit 1
+fi
 STORIES_DIR="$PROJECT_ROOT/project/board/stories"
 TASKS_DIR="$PROJECT_ROOT/project/board/tasks"
 

package/skills/j-commit/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.commit
-description: Polyfill alias of the commit skill under a collision-safe directory name. Identical behavior to /commit — Commit implemented epic, story, or task work using the EST naming convention. Also handles user-action prerequisites and new-epic boundaries. Use after completing any EST work item. Use when the bare /commit form is shadowed by another tool's own built-in command of the same name.
+description: Commit implemented epic, story, or task work using the EST naming convention. Also handles user-action prerequisites and new-epic boundaries. Use after completing any EST work item.
 keywords:
   - commit
   - save
@@ -8,7 +8,6 @@ keywords:
   - done
   - push
   - j-commit
-  - polyfill
 examples:
   - "commit this work"
   - "save my changes"
@@ -17,9 +16,9 @@ examples:
 
 # Commit — Commit Completed Work
 
-This skill is a literal-directory-name duplicate of `skills/commit/`. It exists so that `/j-commit` (and `j.j-commit`) give a guaranteed-unshadowed way to reach the same flow as `/commit`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/commit` alias (Claude Code's native skill resolution is a literal-string, directory-name-based match — see `docs/skill-authoring.md`'s "Invocation Convention").
+`skills/j-commit/` is the **canonical, hand-edited** directory for this skill, per CLAUDE.md's "The Canonical Naming Contract" (the `E50` reopening of 2026-09-09, which promoted `skills/j-commit/` from generated twin to sole canonical form). The `j-` prefix is there for collision safety — a real directory under a distinct name, so a host tool shipping its own same-named built-in command cannot shadow it (Claude Code's native skill resolution is a literal-string, directory-name-based match; see `docs/skill-authoring.md`'s "Invocation Convention").
 
-This file is generated/synced by `scripts/generate-j-alias.sh commit` from `skills/commit/SKILL.md` — do not hand-edit it; re-run the generator instead to pick up source changes.
+> ⚠️ **`scripts/generate-j-alias.sh` was retired by `E50_S14` and no longer exists — there is nothing to run.** This file was previously generated from a bare `skills/commit/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## Inline Mode (called by /do for inline-scoped tasks)
 

package/skills/j-continue/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.continue
-description: Polyfill alias of the continue skill under a collision-safe directory name. Identical behavior to /continue — Check project status across PROJECT_SUMMARY.md, epics, and stories to determine what should be done next. Reports "All done!" if everything is complete. Use when the bare /continue form is shadowed by another tool's own built-in command of the same name.
+description: Check project status across PROJECT_SUMMARY.md, epics, and stories to determine what should be done next. Reports "All done!" if everything is complete.
 keywords:
   - continue
   - next
@@ -8,7 +8,6 @@ keywords:
   - what's next
   - status
   - j-continue
-  - polyfill
 examples:
   - "what should I do next?"
   - "continue with the project"
@@ -17,17 +16,17 @@ examples:
 
 # Continue — Pick Up the Next Work Item
 
-This skill is a literal-directory-name duplicate of `skills/continue/`. It exists so that `/j-continue` (and `j.j-continue`) give a guaranteed-unshadowed way to reach the same flow as `/continue`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/continue` alias (Claude Code's native skill resolution is a literal-string, directory-name-based match — see `docs/skill-authoring.md`'s "Invocation Convention").
+`skills/j-continue/` is the **canonical, hand-edited** directory for this skill, per CLAUDE.md's "The Canonical Naming Contract" (the `E50` reopening of 2026-09-09, which promoted `skills/j-continue/` from generated twin to sole canonical form). The `j-` prefix is there for collision safety — a real directory under a distinct name, so a host tool shipping its own same-named built-in command cannot shadow it (Claude Code's native skill resolution is a literal-string, directory-name-based match; see `docs/skill-authoring.md`'s "Invocation Convention").
 
-This file is generated/synced by `scripts/generate-j-alias.sh continue` from `skills/continue/SKILL.md` — do not hand-edit it; re-run the generator instead to pick up source changes.
+> ⚠️ **`scripts/generate-j-alias.sh` was retired by `E50_S14` and no longer exists — there is nothing to run.** This file was previously generated from a bare `skills/continue/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## Instructions
 
 1. **Check `project/PROJECT_SUMMARY.md`** — Determine if there is outstanding work at the project level.
 
-2. **Check `project/epics/`** — If the project summary is done, check if any epics have remaining work.
+2. **Check `project/board/epics/`** — If the project summary is done, check if any epics have remaining work.
 
-3. **Check `project/stories/`** — If epics are done, check if any stories have remaining work.
+3. **Check `project/board/stories/`** — If epics are done, check if any stories have remaining work.
 
    **Important:** Always check story status within an epic even if the epic itself is marked as done.
 

package/skills/j-deep-dive/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.deep-dive
-description: Polyfill alias of the deep-dive skill under a collision-safe directory name. Identical behavior to /deep-dive — >. Use when the bare /deep-dive form is shadowed by another tool's own built-in command of the same name.
+description: ">."
 metadata:
   prefered_agent: scrum_master
 keywords:
@@ -9,7 +9,6 @@ keywords:
   - "analyze thoroughly"
   - "think through"
   - j-deep-dive
-  - polyfill
 examples:
   - "deep dive on this idea"
   - "let's think through this properly"
@@ -20,9 +19,9 @@ examples:
 
 # /deep-dive — Deep Investigation Workflow
 
-This skill is a literal-directory-name duplicate of `skills/deep-dive/`. It exists so that `/j-deep-dive` (and `j.j-deep-dive`) give a guaranteed-unshadowed way to reach the same flow as `/deep-dive`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/deep-dive` alias (Claude Code's native skill resolution is a literal-string, directory-name-based match — see `docs/skill-authoring.md`'s "Invocation Convention").
+`skills/j-deep-dive/` is the **canonical, hand-edited** directory for this skill, per CLAUDE.md's "The Canonical Naming Contract" (the `E50` reopening of 2026-09-09, which promoted `skills/j-deep-dive/` from generated twin to sole canonical form). The `j-` prefix is there for collision safety — a real directory under a distinct name, so a host tool shipping its own same-named built-in command cannot shadow it (Claude Code's native skill resolution is a literal-string, directory-name-based match; see `docs/skill-authoring.md`'s "Invocation Convention").
 
-This file is generated/synced by `scripts/generate-j-alias.sh deep-dive` from `skills/deep-dive/SKILL.md` — do not hand-edit it; re-run the generator instead to pick up source changes.
+> ⚠️ **`scripts/generate-j-alias.sh` was retired by `E50_S14` and no longer exists — there is nothing to run.** This file was previously generated from a bare `skills/deep-dive/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## Overview