fix(refresh-repo,git-workflow-standards): catch zero-ahead branches; split into prune-branches

AGENTS.md

@@ -17,7 +17,7 @@ This is a **Claude Code plugins repository** containing production-ready hooks f
 | **content-guards** | Pre/PostToolUse | Bash, Write, Edit | Token limits, markdown/README validation, webfetch guard, issue/PR backlog limits, public-repo leakage guard |
 | **git-guards** | PreToolUse | Bash, Edit, Write, NotebookEdit | Blocks dangerous git/gh commands and file edits on main branch |
 | **git-workflows** | Command/Skill | `/sync-main`, `/git-flow-next`, `/troubleshoot-rebase`, `/troubleshoot-precommit`, `/troubleshoot-worktree`, `/pre-commit-architecture` | Local git sync, branching model, and rebase/pre-commit/worktree troubleshooting |
-| **github-workflows** | Command/Skill | `/ship`, `/finalize-pr`, `/refresh-repo` (incl. `--sweep` and `--prune-stale` modes), `/rebase-pr`, `/squash-merge-pr`, `/pr-sweep`, `/resolve-pr-threads`, `/gh-cli-patterns`, `/shape-issues`, `/trigger-ai-reviews` | GitHub PR/issue management workflows, cross-repo workspace sweep, stale-branch pruning, and risk-ranked open-PR sweep-to-zero |
+| **github-workflows** | Command/Skill | `/ship`, `/finalize-pr`, `/refresh-repo`, `/prune-branches` (incl. `--sweep` and `--prune-stale` modes), `/rebase-pr`, `/squash-merge-pr`, `/pr-sweep`, `/resolve-pr-threads`, `/gh-cli-patterns`, `/shape-issues`, `/trigger-ai-reviews` | GitHub PR/issue management workflows, cross-repo workspace sweep, stale-branch pruning, and risk-ranked open-PR sweep-to-zero |
 | **infra-orchestration** | Skill | `/orchestrate-infra`, `/sync-inventory`, `/test-e2e` | Cross-repo infrastructure orchestration for Terraform and Ansible |
 | **code-standards** | Skill | `/code-quality-standards`, `/review-standards` | Code quality standards, documentation formatting, testing philosophy, and review guidelines |
 | **git-standards** | Skill | `/git-workflow-standards`, `/pr-standards` | Git workflow standards, branch hygiene, PR creation guards, workaround vs fix classification, and issue linking |

README.md

@@ -181,7 +181,8 @@ invocation. Skill-based plugins provide slash commands:
 /ship                     # Full automation: commit, push, PR, finalize
 /finalize-pr              # Drive PR to merge-ready state
 /squash-merge-pr          # Validate and squash merge
-/refresh-repo             # Sync main, check PRs, cleanup worktrees
+/refresh-repo             # Sync main, check PRs
+/prune-branches           # Delete dead branches and worktrees
 /wrap-up                  # Session-completion verdict + forward artifact
 /resolve-codeql           # Fix CodeQL security alerts
 /delegate-to-ai           # Route tasks to available AI models

ai-cli-harness-better-practices/ARCHITECTURE.md

@@ -21,8 +21,8 @@ flowchart TD
 
     subgraph optional["Optional git enrichment"]
         refresh["/refresh-repo\n(github-workflows)"]:::external
+        prune["/prune-branches\n(github-workflows)"]:::external
         ghcli["/gh-cli-patterns\n(github-workflows)"]:::external
-        cleangone["/clean_gone\n(commit-commands)"]:::external
     end
 
     subgraph referred["Referred out, never rebuilt"]
@@ -36,7 +36,7 @@ flowchart TD
     wrapup --> handoff
     wrapup --> retro
     wrapup -.->|"if git repo"| refresh
-    wrapup -.->|"if git repo"| cleangone
+    wrapup -.->|"if git repo"| prune
 
     status --> handoff
     status -.->|"if git repo"| ghcli

ai-cli-harness-better-practices/README.md

@@ -65,8 +65,8 @@ This plugin deliberately does not reimplement work that already exists:
 | Prose quality | `elements-of-style:writing-clearly-and-concisely` |
 
 The git-side actions the continuity skills delegate to live in their own
-plugins: `github-workflows:refresh-repo`, `github-workflows:gh-cli-patterns`,
-and `commit-commands:clean_gone`.
+plugin: `github-workflows:refresh-repo`, `github-workflows:prune-branches`,
+and `github-workflows:gh-cli-patterns`.
 
 ## Installation
 

ai-cli-harness-better-practices/skills/session-status/SKILL.md

@@ -296,7 +296,7 @@ to `handoff` and `wrap-up`'s resume blocks, not this dashboard.
   Step 0 and handles conditional repository cleanup.
 - **resume** (this plugin) — cold pickup; reuses this skill's derivation.
 - **replan** (this plugin) — rebuilds a plan this skill shows has drifted.
-- **refresh-repo** (github-workflows) — Checks PR merge-readiness, syncs local
-  main, and cleans worktrees.
+- **refresh-repo** (github-workflows) — Checks PR merge-readiness and syncs local main.
+- **prune-branches** (github-workflows) — Deletes stale branches and worktrees.
 - **retrospecting** (claude-retrospective) — Generates detailed retrospectives
   based on session logs and git diffs.

ai-cli-harness-better-practices/skills/wrap-up/SKILL.md

@@ -84,16 +84,16 @@ skipped" in the summary, and run A2 and A4 as normal. Steps A2 and A4 are the
 part of a wrap-up that always applies.
 
 In a repository, run Steps A1 and A2 **in parallel** (they are independent).
-Step A3 starts as soon as Step A1 completes (depends on its remote prune). Step
-A4 runs after all prior steps finish. Provide a summary of actions taken.
+Step A3 runs after both finish. Provide a summary of actions taken.
 
-### A1. Refresh Repository (repository only)
+### A1. Refresh and Prune Repository (repository only)
 
-Invoke `/refresh-repo` to:
+Invoke `/refresh-repo` to sync, then `/prune-branches` to delete anything
+left with nothing useful:
 
 - Check merge-readiness of any remaining open PRs
 - Sync the local default branch with remote (main on trunk repos, develop on git-flow repos)
-- Clean up stale worktrees (merged PRs, `[gone]` remote branches)
+- Delete stale branches and worktrees — local, remote, or both
 - Report repository state
 
 ### A2. Quick Retrospective
@@ -111,17 +111,7 @@ reporting a full retrospective.
 
 **Requires**: `claude-retrospective` plugin (external). If not installed, skip this step and note it was skipped.
 
-### A3. Clean Gone Branches (repository only)
-
-Invoke `/clean_gone` to remove any local branches whose remote tracking branch has been deleted:
-
-- Identify branches marked `[gone]`
-- Remove associated worktrees
-- Delete the local branches
-
-**Requires**: `commit-commands` plugin (external). If not installed, skip this step and note it was skipped.
-
-### A4. Follow-Up Session Prompt
+### A3. Follow-Up Session Prompt
 
 If `/session-status` in Step 0 surfaced follow-up work, invoke the `/handoff`
 skill to emit the next-session artifact. Pass it the "Recommended Prompt for Next
@@ -159,7 +149,7 @@ Wrap-Up Summary
 
 ## Path B — Resume blocks (plan incomplete)
 
-Skip Path A entirely. Skipping is intentional: `/refresh-repo` prunes stale
+Skip Path A entirely. Skipping is intentional: `/prune-branches` deletes stale
 worktrees, which would delete the in-flight worktree the user needs to resume
 in.
 
@@ -269,15 +259,15 @@ Sequence:
 Closes the gap where `gh pr close --delete-branch` removes only the remote
 branch and leaves the local branch + worktree behind. Reuses the
 worktree-removal command shape from `/troubleshoot-worktree` and aligns with
-`/clean_gone`'s post-removal state.
+`/prune-branches`'s post-removal state.
 
 ## Related Skills
 
 - **handoff** (this plugin) — builds the two-part next-session artifact (goal
-  statement under 4000 chars + full prompt) used by Path A Step A4 and Path B Step B2
-- **refresh-repo** (github-workflows) — PR readiness check + repo sync +
-  worktree cleanup (Path A Step A1 dependency); also provides `--sweep` and
-  `--prune-stale` modes
+  statement under 4000 chars + full prompt) used by Path A Step A3 and Path B Step B2
+- **refresh-repo** (github-workflows) — PR readiness check + default-branch sync (Path A Step A1)
+- **prune-branches** (github-workflows) — stale branch and worktree cleanup
+  (Path A Step A1); also provides `--sweep` and `--prune-stale` modes
 - **shape-issues** (github-workflows) — Shape and create well-structured GitHub
   issues for code/repo defects and features; not for incidents (Zammad, see
   session-status Step 4 and pr-standards)

git-standards/ARCHITECTURE.md

@@ -19,14 +19,15 @@ flowchart LR
     subgraph consumers["Skills that load these standards"]
         SM["/sync-main\n(git-workflows)"]:::external
         RR["/refresh-repo\n(git-workflows)"]:::external
+        PB["/prune-branches\n(git-workflows)"]:::external
         RP["/rebase-pr\n(git-workflows)"]:::external
         SHIP["/ship\n(github-workflows)"]:::external
         FPR["/finalize-pr\n(github-workflows)"]:::external
         SI["/shape-issues\n(github-workflows)"]:::external
     end
 
     GWS -.->|"informs branch ops"| SM
-    GWS -.->|"informs cleanup"| RR
+    GWS -.->|"informs cleanup"| PB
     GWS -.->|"informs merge"| RP
     PS -.->|"informs PR creation"| SHIP
     PS -.->|"informs PR finalization"| FPR

git-standards/skills/git-workflow-standards/SKILL.md

@@ -18,12 +18,15 @@ Create a worktree for the change; remove it when the work is done.
 Every branch with commits MUST have an associated PR.
 Orphaned branches must get a PR or be deleted.
 
-**Stale worktree**: A branch with no open PR, no uncommitted changes, and either a merged PR
-whose `headRefOid` matches local `HEAD`, or a deleted remote (`[gone]`) with no commits ahead
-of the default branch (`git log origin/<default>..HEAD --oneline` is empty). Branches with open
-PRs, local-only branches without merged PRs, local commits beyond the merged PR head, and
-worktrees with uncommitted changes are NEVER stale. Use `git worktree remove` (never `--force`)
-— Git natively blocks removal of dirty worktrees.
+**Stale branch** (worktree-paired, bare local, or remote-only — see
+`prune-branches`, github-workflows, for the full procedure): a non-default
+branch, checked out nowhere, unreferenced by any open PR (`--head` or
+`--base`), with no uncommitted changes (when a worktree exists), and either
+a merged PR whose `headRefOid` matches the branch tip, or zero commits ahead
+of the default branch. Use `git worktree remove` (never `--force`) for
+worktree-paired branches — Git blocks removal of dirty worktrees — and
+`git push origin --delete` for a live remote ref, only after
+`prune-branches`'s pre-push ancestry re-check.
 
 ## Branch Hygiene
 
@@ -53,7 +56,7 @@ Sync workflow (replace `<default>` with the repo's actual default branch — see
 `gh-cli-patterns`, github-workflows):
 
 ```bash
-git fetch origin <default> && git pull origin <default>   # in the <default> worktree
+git pull origin <default>                                   # in the <default> worktree
 git merge origin/<default> --no-edit                       # in the feature worktree
 ```
 
@@ -89,7 +92,8 @@ contradictions, or security-sensitive code.
 ## Related Skills
 
 - **sync-main** (git-workflows) — Syncs the repo's default branch and merges into current or all PR branches
-- **refresh-repo** (github-workflows) — Full repo sync including PR status and worktree cleanup
+- **refresh-repo** (github-workflows) — PR status and default-branch sync
+- **prune-branches** (github-workflows) — Stale branch and worktree cleanup
 - **gh-cli-patterns** (github-workflows) — Canonical default-branch detection (trunk vs git-flow)
 - **pr-standards** (git-standards) — PR creation guards, issue linking, and review standards
 - **git-flow-next** (git-workflows) — Dedicated git-flow-next guide, worktree setup, and promotion steps

git-workflows/skills/sync-main/SKILL.md

@@ -101,7 +101,8 @@ Read files, understand both versions, combine intelligently, stage resolved file
 
 ## Related Skills
 
-- **refresh-repo** (github-workflows) — Full repo sync including PR status and worktree cleanup
+- **refresh-repo** (github-workflows) — PR status and default-branch sync
+- **prune-branches** (github-workflows) — Stale branch and worktree cleanup
 - **rebase-pr** (github-workflows) — Rebase-merge workflow that builds on a synced base branch
 - **promote-release** (github-workflows) — Moves develop to main on git-flow repos; the fast-forward step here only reads main, never pushes it
 - **gh-cli-patterns** (github-workflows) — Canonical default-branch detection (trunk vs git-flow)

git-workflows/skills/troubleshoot-worktree/SKILL.md

@@ -68,4 +68,5 @@ echo "<folder>/" >> .gitignore
 
 - **troubleshoot-rebase** (git-workflows) — Diagnose and recover from git rebase failures
 - **troubleshoot-precommit** (git-workflows) — Troubleshoot pre-commit hook failures
-- **refresh-repo** (github-workflows) — Full repo sync including worktree cleanup
+- **refresh-repo** (github-workflows) — Default-branch sync
+- **prune-branches** (github-workflows) — Worktree and branch cleanup

github-workflows/.claude-plugin/plugin.json

@@ -24,6 +24,7 @@
     "./skills/rebase-pr",
     "./skills/promote-release",
     "./skills/refresh-repo",
+    "./skills/prune-branches",
     "./skills/gh-cli-patterns",
     "./skills/shape-issues",
     "./skills/resolve-pr-threads",

github-workflows/ARCHITECTURE.md

@@ -24,9 +24,10 @@ graph LR
 
 ## 1. Skill Dependency Map
 
-All skills and their cross-plugin dependencies. `/refresh-repo`, `/rebase-pr`,
-`/squash-merge-pr`, `/promote-release`, and `/gh-cli-patterns` are local to this
-plugin (no cross-plugin hop) — `/squash-merge-pr`, `/rebase-pr`, and
+All skills and their cross-plugin dependencies. `/refresh-repo`,
+`/prune-branches`, `/rebase-pr`, `/squash-merge-pr`, `/promote-release`, and
+`/gh-cli-patterns` are local to this plugin (no cross-plugin hop) —
+`/squash-merge-pr`, `/rebase-pr`, and
 `/promote-release` all consume the canonical PR-readiness gate and the
 default-branch detection from `/gh-cli-patterns` directly. On a git-flow repo,
 `/squash-merge-pr` and `/rebase-pr` both refuse a `main`-targeting PR and point
@@ -41,6 +42,7 @@ flowchart TD
     RBP["/rebase-pr"]:::ai
     PRR["/promote-release"]:::ai
     RFR["/refresh-repo"]:::ai
+    PBR["/prune-branches"]:::ai
     GCP["/gh-cli-patterns"]:::ai
     TAR["/trigger-ai-reviews"]:::ai
     SI["/shape-issues"]:::ai
@@ -152,7 +154,7 @@ flowchart TD
         direction TB
         W1["/refresh-repo\n(this plugin)"]:::ai
         W2["/retrospecting quick\n(claude-retrospective, external)"]:::external
-        W3["/clean_gone\n(commit-commands, external)"]:::external
+        W3["/prune-branches\n(this plugin)"]:::ai
         W4["Summary report"]:::ai
 
         W1 --> W3 --> W4

github-workflows/README.md

@@ -8,7 +8,8 @@ See [ARCHITECTURE.md](ARCHITECTURE.md) for integration diagrams and the master s
 
 - **`/ship`** - Full automation: commit, push, create PR(s), and auto-finalize in one command.
 - **`/finalize-pr`** - Finalize PRs for merge: single PR, all repo PRs (`all`), or all org PRs (`org`). Includes bot-authored PRs in all modes.
-- **`/refresh-repo`** - Check PR merge-readiness, sync local repo, and cleanup stale worktrees
+- **`/refresh-repo`** - Check PR merge-readiness and sync the local repo with its default branch
+- **`/prune-branches`** - Delete branches and worktrees with nothing useful, local and remote; optional multi-repo sweep
 - **`/rebase-pr`** - Merge a PR using local git rebase + signed commits + a direct push to its base branch (main on trunk repos, develop on git-flow repos)
 - **`/squash-merge-pr`** - Validate PR readiness and squash merge into its base branch (errors if not ready); refuses on git-flow repos when the base is main
 - **`/promote-release`** - Merge-commit a develop → main promotion PR on a git-flow repo; release-please takes over from there
@@ -32,7 +33,8 @@ claude plugins add jacobpevans-cc-plugins/github-workflows
 /finalize-pr 42           # Finalize specific PR by number
 /finalize-pr all          # Finalize all open PRs in repo (including bots)
 /finalize-pr org          # Finalize all open PRs across org (including bots)
-/refresh-repo             # PR check, sync, worktree cleanup
+/refresh-repo             # PR check, default-branch sync
+/prune-branches           # Delete dead branches and worktrees
 /rebase-pr                # Rebase-merge current branch
 /rebase-pr 42             # Rebase-merge specific PR by number
 /squash-merge-pr          # Validate and squash merge

github-workflows/skills/pr-sweep/SKILL.md

@@ -7,8 +7,8 @@ description: "Drive open PRs toward zero across one or many repos by risk-rankin
 
 Take a pile of open PRs and drive it to zero: merge what is safe, surface what is
 not with a specific reason. This is triage-and-clear, distinct from
-`/refresh-repo --sweep` (which syncs repos and cleans worktrees). This skill acts
-on **open PRs**; that one acts on **repo/worktree state**.
+`/prune-branches --sweep` (which deletes dead branches and worktrees). This
+skill acts on **open PRs**; that one acts on **repo/worktree state**.
 
 It does not reimplement merging. It **risk-ranks**, then hands each merge to
 `/squash-merge-pr` (which itself runs the readiness gate and calls `/finalize-pr`).
@@ -83,5 +83,5 @@ outcome, not a failure.
 
 - **squash-merge-pr** (github-workflows) — performs each merge; this skill decides which.
 - **finalize-pr** (github-workflows) — PR metadata/soft-block handling, via squash-merge-pr.
-- **refresh-repo** (github-workflows) — the repo/worktree sweep; complementary, not this.
+- **prune-branches** (github-workflows) — the repo/worktree sweep; complementary, not this.
 - **promote-release** (github-workflows) — the correct path for held promotion PRs.