@jenga-ai/agent 3.6.0 → 4.0.0

package/skills/j-error/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.error
-description: Polyfill alias of the error skill under a collision-safe directory name. Identical behavior to /error — Guided troubleshooting flow that gathers context about an error — where it occurs, what was attempted, what went wrong, and what was expected. Use when the bare /error form is shadowed by another tool's own built-in command of the same name.
+description: Guided troubleshooting flow that gathers context about an error — where it occurs, what was attempted, what went wrong, and what was expected.
 keywords:
   - error
   - bug
@@ -9,7 +9,6 @@ keywords:
   - debug
   - broken
   - j-error
-  - polyfill
 examples:
   - "I'm getting an error"
   - "help me fix this bug"
@@ -20,9 +19,9 @@ metadata:
 
 # Error — Guided Troubleshooting
 
-This skill is a literal-directory-name duplicate of `skills/error/`. It exists so that `/j-error` (and `j.j-error`) give a guaranteed-unshadowed way to reach the same flow as `/error`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/error` 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-error/` 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-error/` 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 error` from `skills/error/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/error/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-evaluate/SKILL.md

@@ -1,16 +1,15 @@
 ---
 name: j.evaluate
-description: Polyfill alias of the evaluate skill under a collision-safe directory name. Identical behavior to /evaluate — Analyzes example files against a target goal and produces a structured evaluation rapport. Use when the bare /evaluate form is shadowed by another tool's own built-in command of the same name.
+description: Analyzes example files against a target goal and produces a structured evaluation rapport.
 keywords:
   - j-evaluate
-  - polyfill
 ---
 
 # Evaluate
 
-This skill is a literal-directory-name duplicate of `skills/evaluate/`. It exists so that `/j-evaluate` (and `j.j-evaluate`) give a guaranteed-unshadowed way to reach the same flow as `/evaluate`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/evaluate` 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-evaluate/` 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-evaluate/` 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 evaluate` from `skills/evaluate/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/evaluate/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## Input
 

package/skills/j-examplify/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.examplify
-description: Polyfill alias of the examplify skill under a collision-safe directory name. Identical behavior to /examplify — Explains concepts, features, use cases, and patterns based on provided context — a description, scenario, code snippet, or file. Use when the user wants to understand what something is, how it works, when to use it, or wants a concrete example. Use when the bare /examplify form is shadowed by another tool's own built-in command of the same name.
+description: Explains concepts, features, use cases, and patterns based on provided context — a description, scenario, code snippet, or file. Use when the user wants to understand what something is, how it works, when to use it, or wants a concrete example.
 keywords:
   - examplify
   - explain
@@ -8,7 +8,6 @@ keywords:
   - how does
   - understand
   - j-examplify
-  - polyfill
 examples:
   - "explain how this works"
   - "give me an example of X"
@@ -17,9 +16,9 @@ examples:
 
 # Concept Explainer
 
-This skill is a literal-directory-name duplicate of `skills/examplify/`. It exists so that `/j-examplify` (and `j.j-examplify`) give a guaranteed-unshadowed way to reach the same flow as `/examplify`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/examplify` 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-examplify/` 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-examplify/` 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 examplify` from `skills/examplify/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/examplify/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-help/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.help
-description: Polyfill alias of the help skill under a collision-safe directory name. Identical behavior to /help — List all available skills with a short description of what each one does. Also use this skill when the user wants to know what commands or skills are available in the project. Use when the bare /help form is shadowed by another tool's own built-in command of the same name.
+description: List all available skills with a short description of what each one does. Also use this skill when the user wants to know what commands or skills are available in the project.
 keywords:
   - help
   - skills
@@ -8,7 +8,6 @@ keywords:
   - what can you do
   - list skills
   - j-help
-  - polyfill
 examples:
   - "what skills are available?"
   - "show me all commands"
@@ -17,9 +16,9 @@ examples:
 
 # Help — List Available Skills
 
-This skill is a literal-directory-name duplicate of `skills/help/`. It exists so that `/j-help` (and `j.j-help`) give a guaranteed-unshadowed way to reach the same flow as `/help`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/help` 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-help/` 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-help/` 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 help` from `skills/help/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/help/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-idea/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.idea
-description: Polyfill alias of the idea skill under a collision-safe directory name. Identical behavior to /idea — DEPRECATED - use the prefixed 'j-idea' skill instead. Capture a loosely-defined idea to project/ideas.md — a lightweight, "maybe someday" log with no board or promotion overhead. Use when the bare /idea form is shadowed by another tool's own built-in command of the same name.
+description: Capture a loosely-defined idea to project/ideas.md — a lightweight, "maybe someday" log with no board or promotion overhead.
 keywords:
   - idea
   - capture idea
@@ -8,7 +8,6 @@ keywords:
   - brain dump
   - maybe someday
   - j-idea
-  - polyfill
 examples:
   - "capture this as an idea"
   - "log this idea for later"
@@ -20,9 +19,9 @@ metadata:
 
 # Idea — Lightweight Idea Capture
 
-This skill is a literal-directory-name duplicate of `skills/idea/`. It exists so that `/j-idea` (and `j.j-idea`) give a guaranteed-unshadowed way to reach the same flow as `/idea`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/idea` 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-idea/` 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-idea/` 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 idea` from `skills/idea/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/idea/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-improve/SKILL.md

@@ -1,16 +1,15 @@
 ---
 name: j.improve
-description: Polyfill alias of the improve skill under a collision-safe directory name. Identical behavior to /improve — A skill for analyzing a codebase and producing a structured improvement plan toward a defined goal. Use when the bare /improve form is shadowed by another tool's own built-in command of the same name.
+description: A skill for analyzing a codebase and producing a structured improvement plan toward a defined goal.
 keywords:
   - j-improve
-  - polyfill
 ---
 
 # Improve
 
-This skill is a literal-directory-name duplicate of `skills/improve/`. It exists so that `/j-improve` (and `j.j-improve`) give a guaranteed-unshadowed way to reach the same flow as `/improve`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/improve` 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-improve/` 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-improve/` 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 improve` from `skills/improve/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/improve/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-init/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.init
-description: Polyfill alias of the init skill under a collision-safe directory name. Identical behavior to /init — initializes a new project with the standard directory structure, PROJECT_SUMMARY.md, workflow.json, git repo, and gitignore. Use when the built-in "/init" command (e.g. GH Copilot's own init) shadows Jenga's /init alias.
+description: initializes a new project with the standard directory structure, PROJECT_SUMMARY.md, workflow.json, git repo, and gitignore. Use when the built-in "/init" command (e.g. GH Copilot's own init) shadows Jenga's /init alias.
 keywords:
   - init
   - initialize
@@ -8,7 +8,6 @@ keywords:
   - new project
   - scaffold
   - j-init
-  - polyfill
 examples:
   - "initialize a new project"
   - "set up a new workspace"
@@ -17,15 +16,25 @@ examples:
 
 # J-Init — Project Setup (polyfill alias of Init)
 
-This skill is a literal-directory-name duplicate of `skills/init/`. It exists because
-some host tools/harnesses (e.g. GH Copilot) ship their own built-in command literally
-named `/init`, which can shadow or override Jenga AI's own `/init` alias (Claude Code's
-native skill resolution is a literal-string, directory-name-based match — see
-`docs/skill-authoring.md`'s "Invocation Convention"). `/j-init` (and `j.j-init`) give
-users a guaranteed-unshadowed way to reach the exact same setup flow.
-
-Keep this file's instructions in lockstep with `skills/init/SKILL.md` — any change made
-there should be mirrored here.
+`skills/j-init/` is the **sole canonical directory** for this skill. The `j-` prefix is
+there for collision safety: some host tools/harnesses (e.g. GH Copilot) ship their own
+built-in command literally named `/init`, which would shadow a bare `/init` alias, since
+Claude Code's native skill resolution is a literal-string, directory-name-based match —
+see `docs/skill-authoring.md`'s "Invocation Convention". Invoke it as `j.init` or
+`/j-init`.
+
+> **This file was previously described as a duplicate of `skills/init/`, with an
+> instruction to keep the two in lockstep. That instruction is void.** `E50_S15_T04`
+> deleted every bare-name `skills/<name>/` directory on 2026-09-19, making
+> `skills/j-<name>/` the sole canonical form (see `docs/skill-authoring.md`'s "The
+> Canonical Naming Contract"), and `scripts/generate-j-alias.sh` — which had excluded this
+> hand-maintained pair from generation anyway — was retired by `E50_S14_T01`. There is no
+> second copy to mirror a change into, and none should be created. Edit this file directly.
+>
+> Corrected by `E42_S07_T01`'s follow-up, per
+> `project/rapports/problems/E42_S07_T01-j-init-skill-md-lockstep-instruction-still-stale.md`.
+> The same correction already landed one level down, in
+> `skills/j-init/scripts/apply-scaffold-visibility.sh`.
 
 ## Instructions
 

package/skills/j-init/scripts/apply-scaffold-visibility.sh

@@ -14,12 +14,14 @@
 # skills/j-distribute/CONFIG_SCHEMA.md's "Scaffold visibility" section for the
 # full rationale.
 #
-# This is skills/j-init/'s own copy of skills/init/scripts/apply-scaffold-visibility.sh
-# (E31_S07_T03) — skills/j-init/ is a separate, hand-maintained directory, not
-# auto-synced with skills/init/ (scripts/generate-j-alias.sh explicitly excludes
-# this pair), and is the copy that actually ships to public-GitHub-mirror and
-# npm-package consumers. Keep this file's logic in lockstep with skills/init/'s
-# copy — any behavioral change made there should be mirrored here.
+# This file is the sole copy. It was added by E31_S07_T03 as skills/j-init/'s own
+# hand-maintained duplicate of a then-existing skills/init/scripts/ copy, with an
+# instruction to keep the two in lockstep. That instruction is void: E50_S15_T04
+# deleted every bare-name skills/<name>/ directory on 2026-09-19, making
+# skills/j-<name>/ the sole canonical form (see docs/skill-authoring.md's "The
+# Canonical Naming Contract"), and scripts/generate-j-alias.sh — which had excluded
+# this pair from generation as hand-maintained — was itself retired by E50_S14_T01.
+# There is no second copy to mirror a change into, and none should be created.
 #
 # Usage:
 #   apply-scaffold-visibility.sh <mode> [project_root]

package/skills/j-jbp/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.jbp
-description: Polyfill alias of the jbp skill under a collision-safe directory name. Identical behavior to /jbp — Scaffold the project using the JengaBasePlate boilerplate repo template from https://github.com/samwelmunga/JengaBasePlate.git. Use when the bare /jbp form is shadowed by another tool's own built-in command of the same name.
+description: Scaffold the project using the JengaBasePlate boilerplate repo template from https://github.com/samwelmunga/JengaBasePlate.git.
 keywords:
   - jbp
   - boilerplate
@@ -8,7 +8,6 @@ keywords:
   - template
   - jenga base
   - j-jbp
-  - polyfill
 examples:
   - "scaffold with JengaBasePlate"
   - "set up the base template"
@@ -17,9 +16,9 @@ examples:
 
 # JBP — JengaBasePlate Scaffold
 
-This skill is a literal-directory-name duplicate of `skills/jbp/`. It exists so that `/j-jbp` (and `j.j-jbp`) give a guaranteed-unshadowed way to reach the same flow as `/jbp`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/jbp` 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-jbp/` 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-jbp/` 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 jbp` from `skills/jbp/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/jbp/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-lgtm/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.lgtm
-description: Polyfill alias of the lgtm skill under a collision-safe directory name. Identical behavior to /lgtm — Approve and commit the current work, then continue to the next task. Shortcut that chains /commit followed by /continue. Use when the bare /lgtm form is shadowed by another tool's own built-in command of the same name.
+description: Approve and commit the current work, then continue to the next task. Shortcut that chains /commit followed by /continue.
 keywords:
   - lgtm
   - approve
@@ -8,7 +8,6 @@ keywords:
   - done
   - commit and continue
   - j-lgtm
-  - polyfill
 examples:
   - "lgtm, commit this"
   - "looks good, move on"
@@ -17,9 +16,9 @@ examples:
 
 # LGTM — Approve, Commit, and Continue
 
-This skill is a literal-directory-name duplicate of `skills/lgtm/`. It exists so that `/j-lgtm` (and `j.j-lgtm`) give a guaranteed-unshadowed way to reach the same flow as `/lgtm`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/lgtm` 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-lgtm/` 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-lgtm/` 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 lgtm` from `skills/lgtm/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/lgtm/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-pi-plan/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.pi-plan
-description: Polyfill alias of the pi-plan skill under a collision-safe directory name. Identical behavior to /pi-plan — Define or expand project Epics in PROJECT_SUMMARY.md. Use this at the start of a project to establish its foundation, AND whenever the user wants to add major new features, plan a significant new area of work, or make epic-level changes to an existing project. Trigger whenever you hear things like "new feature area", "big change", "new epic", "expand the project", "add a major capability", or "plan a new phase" — even mid-project. Use when the bare /pi-plan form is shadowed by another tool's own built-in command of the same name.
+description: Define or expand project Epics in PROJECT_SUMMARY.md. Use this at the start of a project to establish its foundation, AND whenever the user wants to add major new features, plan a significant new area of work, or make epic-level changes to an existing project. Trigger whenever you hear things like "new feature area", "big change", "new epic", "expand the project", "add a major capability", or "plan a new phase" — even mid-project.
 keywords:
   - epic
   - template
@@ -8,7 +8,6 @@ keywords:
   - new feature area
   - project structure
   - j-pi-plan
-  - polyfill
 examples:
   - "add a new epic for X"
   - "expand the project with a new feature area"
@@ -19,9 +18,9 @@ metadata:
 
 # Pi-plan — Define and Expand Project Epics
 
-This skill is a literal-directory-name duplicate of `skills/pi-plan/`. It exists so that `/j-pi-plan` (and `j.j-pi-plan`) give a guaranteed-unshadowed way to reach the same flow as `/pi-plan`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/pi-plan` 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-pi-plan/` 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-pi-plan/` 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 pi-plan` from `skills/pi-plan/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/pi-plan/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## When to use this skill
 

package/skills/j-proceed/SKILL.md

@@ -1,13 +1,12 @@
 ---
 name: j.proceed
-description: Polyfill alias of the proceed skill under a collision-safe directory name. Identical behavior to /proceed — Review project progress by checking epics and stories, optionally consulting PROJECT_SUMMARY.md and WARP.md, then continue executing the project plan. Use when the bare /proceed form is shadowed by another tool's own built-in command of the same name.
+description: Review project progress by checking epics and stories, optionally consulting PROJECT_SUMMARY.md and WARP.md, then continue executing the project plan.
 keywords:
   - proceed
   - review progress
   - check epics
   - continue executing
   - j-proceed
-  - polyfill
 examples:
   - "proceed with the plan"
   - "review progress and continue"
@@ -18,9 +17,9 @@ metadata:
 
 # Proceed — Resume Project Execution
 
-This skill is a literal-directory-name duplicate of `skills/proceed/`. It exists so that `/j-proceed` (and `j.j-proceed`) give a guaranteed-unshadowed way to reach the same flow as `/proceed`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/proceed` 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-proceed/` 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-proceed/` 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 proceed` from `skills/proceed/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/proceed/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-publish/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.publish
-description: Polyfill alias of the publish skill under a collision-safe directory name. Identical behavior to /publish — Configure, validate, and orchestrate scaffolded release workflows through a single `/publish` entry point with bounded sub-commands. Use when the bare /publish form is shadowed by another tool's own built-in command of the same name.
+description: Configure, validate, and orchestrate scaffolded release workflows through a single `/publish` entry point with bounded sub-commands.
 keywords:
   - publish
   - deploy
@@ -12,7 +12,6 @@ keywords:
   - staged publishing
   - stage
   - j-publish
-  - polyfill
 examples:
   - "publish setup --target staging-appstore"
   - "publish setup --type mobile-ios"
@@ -42,9 +41,9 @@ metadata:
 
 # Publish — Deployment Pipeline Orchestrator
 
-This skill is a literal-directory-name duplicate of `skills/publish/`. It exists so that `/j-publish` (and `j.j-publish`) give a guaranteed-unshadowed way to reach the same flow as `/publish`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/publish` 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-publish/` 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-publish/` 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 publish` from `skills/publish/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/publish/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 `/publish` is the single entry point for release workflows in this repository. It wires configuration validation, setup, gated deployment, release-note drafting, and ledger history into one end-to-end flow, and dispatches the final publish step to a per-type adapter.
 

package/skills/j-publish/scripts/run_gates.sh

@@ -292,7 +292,7 @@ run_command_capture() {
   local command="$1"
   LAST_GATE_COMMAND="$command"
   set +e
-  RUN_OUTPUT="$(bash -lc "$command" 2>&1)"
+  RUN_OUTPUT="$(bash -c "$command" 2>&1)"
   RUN_STATUS=$?
   set -e
 }

package/skills/j-reconcile/SKILL.md

@@ -1,19 +1,18 @@
 ---
 name: j.reconcile
-description: Polyfill alias of the reconcile skill under a collision-safe directory name. Identical behavior to /reconcile — Reconcile the scrum board with actual implementation state. Cross-checks every task's board status against git history and worktrees, merges orphaned worktree branches, demotes unimplemented "Done" items, promotes secretly-implemented items, flags code with no board provenance and offers /uncharted segment for it, and cleans stale entries from todo.md. Use when the board feels out of sync, after a big merge session, when tasks were completed outside the normal workflow, or when todo.md has grown stale. Trigger on phrases like "sync the board", "clean up the board", "reconcile", "board is out of date", "todo is stale", or "check what's really done". Use when the bare /reconcile form is shadowed by another tool's own built-in command of the same name.
+description: Reconcile the scrum board with actual implementation state. Cross-checks every task's board status against git history and worktrees, merges orphaned worktree branches, demotes unimplemented "Done" items, promotes secretly-implemented items, flags code with no board provenance and offers /uncharted segment for it, and cleans stale entries from todo.md. Use when the board feels out of sync, after a big merge session, when tasks were completed outside the normal workflow, or when todo.md has grown stale. Trigger on phrases like "sync the board", "clean up the board", "reconcile", "board is out of date", "todo is stale", or "check what's really done".
 metadata:
   prefered_agent: scrum-master
 output_types: id_list
 keywords:
   - j-reconcile
-  - polyfill
 ---
 
 # Reconcile — Board ↔ Code Synchronisation
 
-This skill is a literal-directory-name duplicate of `skills/reconcile/`. It exists so that `/j-reconcile` (and `j.j-reconcile`) give a guaranteed-unshadowed way to reach the same flow as `/reconcile`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/reconcile` 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-reconcile/` 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-reconcile/` 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 reconcile` from `skills/reconcile/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/reconcile/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 Walks the full board (epics → stories → tasks), verifies each item's status against what actually exists in git, and fixes any drift. Also cleans `project/todo.md` of entries that are already done. Then runs the same check in reverse — code that exists with no board item and no EST-tagged commit behind it — and offers `/uncharted segment` for what it finds.
 
@@ -136,7 +135,41 @@ in-scope tasks when scoped) whose status is **not** a completed status (Pending,
 2. **Check documentation artefacts** as in phase 2.
 3. **Spot-check acceptance criteria** against the codebase.
 
-If implementation **is confirmed**:
+Before treating a matching commit as grounds to promote, run two more checks. These exist because
+a commit referencing a task ID is evidence the code was *touched*, not evidence it is *finished* —
+a separate, still-running `/do` pipeline for this exact task may have a real fix sitting unmerged
+in a worktree while an earlier, incomplete commit already landed on the branch this `/reconcile`
+pass is reading. This is the exact race documented in
+`project/rapports/problems/E40_S01_T05-premature-main-reconcile-vs-worktree-fix.md` — a `/reconcile`
+pass promoted a task to `Passed`/`Done` from a matching commit alone while a fallback developer/tester
+pipeline for that same task still had its bugfix unmerged on a worktree branch.
+
+4. **Check for an active concurrency-slot holder** — glob `project/queue/concurrency-slots-*.json`
+   (there can be several; one per orchestrating session, per `skills/j-do/SKILL.md`'s
+   `### 4.4. Developer Concurrency Slot Enforcement`). For each file found, check both
+   `.developer.holders` and `.tester.holders` for a key matching this task's id (`E##_S##_T##`) —
+   or, if this task belongs to a story-bundle dispatch, the containing story's id (`E##_S##`),
+   since a bundle acquires one shared slot keyed to the story id rather than one per task (`### 1.5`
+   step 3 of that skill). A matching key means a developer or tester subagent for this exact item is
+   (or very recently was) live in another session.
+5. **Check for an unmerged worktree or branch** — run `git worktree list` and `git branch --all`,
+   and look for an entry matching this task's `<E##_S##_T##-short-slug>` naming convention
+   (`skills/j-do/SKILL.md`'s worktree-naming convention, e.g. its Light Execution Path and Fallback
+   to Full Task-Scope Pipeline sections) that has not yet been merged into the branch this
+   `/reconcile` run is executing against. A match means real work for this task exists on a branch
+   this reconcile pass hasn't accounted for yet.
+
+If **either** check 4 or 5 matches, skip promotion for this task:
+- Leave the task's status exactly as it is now — do not touch `date_started`, `date_completed`, or
+  its `project/todo.md` entry.
+- Do **not** merge the branch/worktree found in check 5 yourself — that is a live pipeline's own
+  work-in-progress, not an orphaned branch like phase 2's merge case.
+- Report it in the reconcile report as **"likely still in-flight — skipped"** (see
+  `assets/report_format.md`'s "⏳ IN-FLIGHT — SKIPPED" section) — not silently promoted, and not
+  silently left unmentioned.
+- Continue to the next task in Phase 3 — this is a per-task skip, not a phase abort.
+
+If implementation **is confirmed** and **neither** check 4 nor 5 matched:
 - Update the task's status to **Passed** in its board file.
 - Set `date_completed` to today (ISO 8601).
 - If the task is listed in `project/todo.md`, **comment it out** by wrapping the line:

package/skills/j-reconcile/assets/report_format.md

@@ -18,6 +18,10 @@ Scope: <resolved scope — see forms below>
 ⬆️  PROMOTED (were incomplete → now Passed)
    🔧 E##_S##_T## · <Task Title>  — commits found, acceptance criteria met
 
+⏳ IN-FLIGHT — SKIPPED (implementation confirmed by commit, but not promoted — active work appears ongoing)
+   🔧 E##_S##_T## · <Task Title>  — concurrency-slot holder found in <concurrency-slots-file>
+   🔧 E##_S##_T## · <Task Title>  — unmerged branch <branch-name>
+
 🔄 ROLL-UP CHANGES
    📖 E##_S## · <Story Title>  — <old status> → <new status>
    📦 E## · <Epic Title>  — <old status> → <new status>
@@ -51,6 +55,13 @@ Scope: <resolved scope — see forms below>
   own epics/stories/tasks only — not the whole board's.
 - Omit any section that has zero items (e.g. if nothing was demoted, skip the DEMOTED block entirely).
 - The MERGED section should include the branch name that was merged.
+- The IN-FLIGHT — SKIPPED section is distinct from both PROMOTED and the ordinary "implementation
+  not confirmed, no action" case (which is never reported at all): it means Phase 3 found a
+  matching commit (implementation confirmed) but withheld promotion because an active
+  concurrency-slot holder or an unmerged matching worktree/branch was also found — see
+  `/reconcile`'s Phase 3. Name the specific reason found (the concurrency-slots file, or the
+  branch/worktree name) so the report is checkable, not just asserted. Omit this section entirely
+  when no task was skipped for this reason.
 - The TODO CLEANUP section is always shown if `project/todo.md` existed at the start, even if zero changes were made (in that case show all counts as 0).
 - If `project/todo.md` did not exist, omit the TODO CLEANUP section.
 - The DOD GAPS section is omitted if no completed stories have unchecked DoD checkboxes.

package/skills/j-reconcile/scripts/detect-unlinked-code.sh

@@ -143,7 +143,7 @@
 #   --board-dir <dir>    Board directory to consult.
 #                        Default: <repo-root>/project/board
 #   --resolver <path>    Path to resolve-segment-target.sh.
-#                        Default: ../../uncharted/scripts/resolve-segment-target.sh
+#                        Default: ../../j-uncharted/scripts/resolve-segment-target.sh
 #   --exclude <glob>     Additional exclusion, matched against the repo-relative
 #                        path with shell-glob semantics. Repeatable.
 #   --limit N            Cap on files listed per group. Default 10. 0 = unlimited.
@@ -292,7 +292,7 @@ REPO_ROOT=$(cd -- "$REPO_ROOT" && pwd -P)
 [ -n "$BOARD_DIR" ] || BOARD_DIR="$REPO_ROOT/project/board"
 
 # --- the borrowed linkage check -------------------------------------------------------------
-[ -n "$RESOLVER" ] || RESOLVER="$SCRIPT_DIR/../../uncharted/scripts/resolve-segment-target.sh"
+[ -n "$RESOLVER" ] || RESOLVER="$SCRIPT_DIR/../../j-uncharted/scripts/resolve-segment-target.sh"
 [ -f "$RESOLVER" ] || die 4 "board-linkage checker not found: $RESOLVER
   This script deliberately has no fallback implementation -- see the header. Restore
   skills/j-uncharted/scripts/resolve-segment-target.sh or pass --resolver <path>."

package/skills/j-reconcile-origin/SKILL.md

@@ -1,13 +1,12 @@
 ---
 name: j.reconcile-origin
-description: Polyfill alias of the reconcile-origin skill under a collision-safe directory name. Identical behavior to /reconcile-origin — Sync the current (or specified) branch with origin by rebasing local commits on top of the latest upstream state. Use when the bare /reconcile-origin form is shadowed by another tool's own built-in command of the same name.
+description: Sync the current (or specified) branch with origin by rebasing local commits on top of the latest upstream state.
 keywords:
   - "sync branch"
   - "rebase origin"
   - "reconcile origin"
   - "pull rebase"
   - j-reconcile-origin
-  - polyfill
 examples:
   - "sync my branch with origin"
   - "rebase local commits on top of origin"
@@ -17,9 +16,9 @@ examples:
 
 # Reconcile Origin
 
-This skill is a literal-directory-name duplicate of `skills/reconcile-origin/`. It exists so that `/j-reconcile-origin` (and `j.j-reconcile-origin`) give a guaranteed-unshadowed way to reach the same flow as `/reconcile-origin`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/reconcile-origin` 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-reconcile-origin/` 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-reconcile-origin/` 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 reconcile-origin` from `skills/reconcile-origin/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/reconcile-origin/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 Use this skill to rebase local work on top of the latest `origin/<branch>` state without re-implementing git logic inline.
 

package/skills/j-redo/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: j.redo
-description: Polyfill alias of the redo skill under a collision-safe directory name. Identical behavior to /redo — Redo parts or entire previous implementations identified by a commit SHA or an Epic/Story number (e.g. E01, E02_S03). Expects an identifier and a description of what to redo and why. Use when the user wants to revisit, rework, or rewrite previously completed work, including updating all affected documentation. Use when the bare /redo form is shadowed by another tool's own built-in command of the same name.
+description: Redo parts or entire previous implementations identified by a commit SHA or an Epic/Story number (e.g. E01, E02_S03). Expects an identifier and a description of what to redo and why. Use when the user wants to revisit, rework, or rewrite previously completed work, including updating all affected documentation.
 keywords:
   - redo
   - rework
@@ -8,7 +8,6 @@ keywords:
   - revisit
   - redo task
   - j-redo
-  - polyfill
 examples:
   - "redo the login implementation"
   - "rewrite story E02_S01"
@@ -19,9 +18,9 @@ metadata:
 
 # Redo — Rework a Previous Implementation
 
-This skill is a literal-directory-name duplicate of `skills/redo/`. It exists so that `/j-redo` (and `j.j-redo`) give a guaranteed-unshadowed way to reach the same flow as `/redo`, even if a host tool's own built-in command of the same name would otherwise shadow or override the bare `/redo` 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-redo/` 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-redo/` 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 redo` from `skills/redo/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/redo/SKILL.md` source; `E50_S15` deleted that directory. This file is now the sole canonical, hand-edited source for this skill — edit it directly.
 
 ## Input Format