fix(branch): cleanup --local keeps branches whose sibling upstream was deleted

A local branch whose upstream sibling was deleted on the remote counted as merged when its tip was reachable from the deleted ref's last known commit, so cleanup --local removed it although git branch -d would refuse. The plan now asks git itself for each candidate, in the same order the delete runs, and skips a branch git would not delete; the README states the rule.

🎯 Fix: 93 %
💥 Break: 3 %
💸 Cost: –
⏱️ Time: –
🛡️ Security: 100 %
🏆 Score: 90
🚦 Gate: ✅ 90/5, cost and time <= 100, security 100 %

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

README.md

@@ -80,7 +80,7 @@ versioning features it can drive **end-to-end workflows**:
 | `pkgmgr worktree flow clear [PATH] [--json]` | Removes the merge flow |
 | `pkgmgr worktree cleanup [--apply]` | Removes clean worktrees whose commits are merged or pushed: pinned `worktree-fini` hook, compose stack, checkout; the branch stays |
 | `pkgmgr branch cleanup [--apply]` | Removes merged branches that no worktree holds, locally and on the remotes |
-| `pkgmgr branch cleanup --local [--apply] [--json] [--merged-into REF]...` | Deletes only local branches whose tip is an ancestor of the remote-tracking default or of a `--merged-into` REF, each with `git update-ref --no-deref -d` against the planned sha and then its `branch.<name>` section in the repository's own config file (`git config --file <git common dir>/config`; a section it cannot remove is noted on the done item), also when the branch has an upstream or remote copy. Every git call of `--local` runs without any inherited `GIT_*` variable but `GIT_CEILING_DIRECTORIES`, which only narrows repository discovery, so a directory below a ceiling is never resolved to the repository above it; only the config reads of `deleteMerged` and of the upstreams run twice, both with the system config: once with the caller's `GIT_CONFIG_GLOBAL`, `GIT_CONFIG_SYSTEM`, `GIT_CONFIG_PARAMETERS` and `GIT_CONFIG_COUNT` with its `GIT_CONFIG_KEY_<n>` and `GIT_CONFIG_VALUE_<n>`, once without any of them, without `XDG_CONFIG_HOME` and with `HOME` set to the passwd home, and a branch either read keeps stays, so the environment can add keeps but never remove one. A `--merged-into` REF must name exactly one branch or remote-tracking ref, as `git rev-parse --symbolic-full-name` resolves it, in every scanned repository git can read; `X~0`, `X^0`, `X@{0}`, a sha, a range or an unknown ref stops the run. The default comes from `origin`, or from the only remote when there is no `origin`: the ref `refs/remotes/<remote>/HEAD`, else `main`, else `master` resolves to, every symref step inside `refs/remotes/<remote>/`, so never a local branch or `HEAD`; without one, for example with several remotes and no `origin`, the repository is refused, also under `--merged-into`; so is one whose `refs`, `packed-refs`, `reftable`, `logs` or `logs/refs` is a symlink (git-new-workdir), one with a symlink anywhere below `refs/`, `reftable/` or `logs/refs/` (for example `refs/heads/team` linked to another clone's heads), one whose git dir is neither its git common dir nor directly under `<common>/worktrees/` (a registration moved elsewhere), or one whose git output is not UTF-8. The repository is the one the current directory belongs to, also in a submodule or with a separate git dir; one whose main worktree belongs to another repository (`core.worktree`), whose git dir is neither its git common dir nor directly under `<common>/worktrees/`, or whose path is not UTF-8 is refused with exit 2. Skips a symbolic branch, every branch a symbolic ref anywhere under `refs/` (also a tag or remote-tracking one) or under the main worktree's or any registration's `refs/worktree/` points to, a branch that is itself a `--merged-into` target, a branch a worktree holds or that the HEAD of the main repository or of any `worktrees/<id>` registration names (also one `git worktree list` omits or whose id is no valid ref name, read through `git --git-dir=<dir> symbolic-ref HEAD`, so also under reftable), one a rebase or bisect in any worktree works on, one merged only by patch or PR, and, as `git branch --delete-merged` keeps them, one whose `branch.<name>.deleteMerged` is false in the config of any worktree (also its `config.worktree` or an `includeIf "onbranch:..."` file) or in the system config file, and the local upstream, as git's `%(upstream)` resolves it in any worktree, of any branch that stays, also of one that `--branch` or `--exclude` leaves out, each shown as kept with its reason; these holds are read through the git common dir, whichever worktree is scanned, and a registration, symbolic ref, HEAD or state file they cannot read refuses the repository; when a repository vanishes, moves or stops being readable, or its default or a `--merged-into` target stops resolving mid-run, its later items are skipped with that reason and the plan is still printed. A repository git or the filesystem fails on while planning (for example a dangling `.git` file under `--all`) is refused with that reason and the run goes on. The plan, refused repositories included, is printed (as JSON with `--json`), and the run exits 1 when an item failed, else 2 when a repository was refused, else 0. It stops with a message on stderr, no plan and exit 2 in exactly these cases: without `--all`, the current directory is not inside a git repository, its git dir is neither its git common dir nor directly under `<common>/worktrees/`, its main worktree belongs to another repository (`core.worktree`), or its path or git output is not UTF-8; `--apply` outside the host PID namespace; a `--merged-into` REF refused as above; a `--branch` that matches no item. Meant for working clones and their worktrees, not for a bare server repository. Not mirrored from `git branch --delete-merged`: git also keeps a branch whose push would update its own upstream; `--local` does not. Known residuals: a worktree, rebase or symbolic ref that starts holding a branch between its last re-check and its `update-ref -d` is not seeLine truncated
+| `pkgmgr branch cleanup --local [--apply] [--json] [--merged-into REF]...` | Deletes only local branches whose tip is an ancestor of the remote-tracking default or of a `--merged-into` REF, each with `git update-ref --no-deref -d` against the planned sha and then its `branch.<name>` section in the repository's own config file (`git config --file <git common dir>/config`; a section it cannot remove is noted on the done item), also when the branch has an upstream or remote copy. Every git call of `--local` runs without any inherited `GIT_*` variable but `GIT_CEILING_DIRECTORIES`, which only narrows repository discovery, so a directory below a ceiling is never resolved to the repository above it; only the config reads of `deleteMerged` and of the upstreams run twice, both with the system config: once with the caller's `GIT_CONFIG_GLOBAL`, `GIT_CONFIG_SYSTEM`, `GIT_CONFIG_PARAMETERS` and `GIT_CONFIG_COUNT` with its `GIT_CONFIG_KEY_<n>` and `GIT_CONFIG_VALUE_<n>`, once without any of them, without `XDG_CONFIG_HOME` and with `HOME` set to the passwd home, and a branch either read keeps stays, so the environment can add keeps but never remove one. A `--merged-into` REF must name exactly one branch or remote-tracking ref, as `git rev-parse --symbolic-full-name` resolves it, in every scanned repository git can read; `X~0`, `X^0`, `X@{0}`, a sha, a range or an unknown ref stops the run. The default comes from `origin`, or from the only remote when there is no `origin`: the ref `refs/remotes/<remote>/HEAD`, else `main`, else `master` resolves to, every symref step inside `refs/remotes/<remote>/`, so never a local branch or `HEAD`; without one, for example with several remotes and no `origin`, the repository is refused, also under `--merged-into`; so is one whose `refs`, `packed-refs`, `reftable`, `logs` or `logs/refs` is a symlink (git-new-workdir), one with a symlink anywhere below `refs/`, `reftable/` or `logs/refs/` (for example `refs/heads/team` linked to another clone's heads), one whose git dir is neither its git common dir nor directly under `<common>/worktrees/` (a registration moved elsewhere), or one whose git output is not UTF-8. The repository is the one the current directory belongs to, also in a submodule or with a separate git dir; one whose main worktree belongs to another repository (`core.worktree`), whose git dir is neither its git common dir nor directly under `<common>/worktrees/`, or whose path is not UTF-8 is refused with exit 2. Skips a symbolic branch, every branch a symbolic ref anywhere under `refs/` (also a tag or remote-tracking one) or under the main worktree's or any registration's `refs/worktree/` points to, a branch that is itself a `--merged-into` target, a branch a worktree holds or that the HEAD of the main repository or of any `worktrees/<id>` registration names (also one `git worktree list` omits or whose id is no valid ref name, read through `git --git-dir=<dir> symbolic-ref HEAD`, so also under reftable), one a rebase or bisect in any worktree works on, one merged only by patch or PR, and, as `git branch --delete-merged` keeps them, one whose `branch.<name>.deleteMerged` is false in the config of any worktree (also its `config.worktree` or an `includeIf "onbranch:..."` file) or in the system config file, and the local upstream, as git's `%(upstream)` resolves it in any worktree, of any branch that stays, also of one that `--branch` or `--exclude` leaves out, each shown as kept with its reason; these holds are read through the git common dir, whichever worktree is scanned, and a registration, symbolic ref, HEAD or state file they cannot read refuses the repository; when a repository vanishes, moves or stops being readable, or its default or a `--merged-into` target stops resolving mid-run, its later items are skipped with that reason and the plan is still printed. A repository git or the filesystem fails on while planning (for example a dangling `.git` file under `--all`) is refused with that reason and the run goes on. The plan, refused repositories included, is printed (as JSON with `--json`), and the run exits 1 when an item failed, else 2 when a repository was refused, else 0. It stops with a message on stderr, no plan and exit 2 in exactly these cases: without `--all`, the current directory is not inside a git repository, its git dir is neither its git common dir nor directly under `<common>/worktrees/`, its main worktree belongs to another repository (`core.worktree`), or its path or git output is not UTF-8; `--apply` outside the host PID namespace; a `--merged-into` REF refused as above; a `--branch` that matches no item (also one that exists only on a remote). Meant for working clones and their worktrees, not for a bare server repository. Not mirrored from `git branch --delete-merged`: git also keeps a branch whose push would update its own upstream; `--local` does not. A branch is deleted before its planned local upstream; right before each delete its holds and then itLine truncated
 | `pkgmgr branch tree [--format json\|yaml] [--output FILE]` | Writes every managed repository's branches and worktrees with their cleanup state, without fetching |
 | `pkgmgr gc [--all] [--apply]` | Both cleanups in one pass, for the current repository or every managed one |
 | `pkgmgr gc --report [--all] [--root DIR] [--threshold-mb MB] [--docker] [--json]` | Read-only disk inventory: worktree sizes, changes a cleanup would keep, `--root` children, core dumps, docker usage, free space per filesystem |