claude-code-repo-migration

name	claude-code-repo-migration
description	Move or rename a git repo on disk without losing its Claude Code history — remap the session dir (~/.claude/projects/<slug>/) and the ~/.claude.json projects key so every past session still resumes from the new path with trust, allowedTools and MCP servers intact, and repair the git worktrees the move breaks. Use when moving a repo to a different parent folder, renaming the org/parent directory, reorganising ~/projects, or after a move when: `claude --resume` shows no sessions / the session picker is empty at the new path, the trust dialog or project onboarding reappears, allowedTools or MCP servers were 'forgotten', auto-memory looks empty, or `git worktree list` / a worktree's git commands break. Covers the slug rule people get wrong (EVERY non-alphanumeric char becomes '-', not just '/'), which extra slug dirs a repo owns, backup-then-mutate ordering, and the fact that ~/.claude.json is live-rewritten by every running session.
metadata	{"author":"stealth-factory","co-author":"wiiiimm","version":"1.0.0"}

Move a repo without losing its Claude Code sessions

A plain mv of a repo works fine for git and breaks everything Claude Code keeps about that repo. Nothing errors — the sessions simply stop appearing, the trust dialog comes back, and the old transcripts sit in a directory nothing looks at any more. This skill is the remap that makes the move invisible.

Commands live in reference/playbook.md; three helpers live in scripts/ — slug derivation, the worktree move plan, and the registry remap. This body is the model and the rules.

The three things, and only one of them is the repo

#	Thing	Where	If you skip it
1	The repo	~/projects/<parent>/<repo>	—
2	Session metadata	~/.claude/projects/<SLUG>/	every past session disappears from the picker; auto-memory goes with it
3	The home registry	~/.claude.json → projects["<abs path>"]	trust dialog + onboarding reappear; allowedTools, mcpServers, mcpContextUris are gone

They are independent. Moving only the repo (2 and 3 left behind) is the common accident — and it is silent.

If the repo has already been moved, which is how most people get here, the forward procedure does not apply: it assumes the old path still exists and would try to move a repo that is gone. Go to step 8 of the playbook — the metadata is untouched, so it is the same remap minus the repo move. Nothing is lost by having waited; the slug dir still holds every transcript. Recover the old path by enumerating the projects keys in ~/.claude.json that no longer exist on disk, then confirm which is this repo against a transcript's cwd — the one place that field is the right evidence, since you are identifying a path rather than deriving a slug from it. (Orphaned keys are common: the machine this was written on had eight, left by an earlier move.)

Do not git worktree prune in this state. Every moved worktree looks prunable to git until the repair runs, and pruning destroys linkage that repair can no longer restore — verified.

The slug dir holds more than transcripts:

~/.claude/projects/<SLUG>/
  <uuid>.jsonl            transcript          <uuid>/subagents/
  <uuid>.jsonl.wakatime   sidecar             <uuid>/tool-results/
  memory/                 auto-memory         <uuid>/remote-agents/

Count sessions with *.jsonl; move or back up the whole directory — the per-session subdirectories are easy to miss with a glob.

The slug rule (the one people get wrong)

Every character outside [A-Za-z0-9] becomes -. Case is preserved.

/home/u/projects/my_app.v2   →  -home-u-projects-my-app-v2
/home/u/proj/repo/.claude/worktrees/x  →  -home-u-proj-repo--claude-worktrees-x

Provenance: probed live on Claude Code 2.1.233 — a session started in …/tmp/Slug_Test.dir with space produced -home-williamli--claude-jobs-…-tmp-Slug-Test-dir-with-space (_, . and the space all became -; capitals survived). Independently confirmed by 4 real worktree slug dirs where .claude appears as -claude, and asserted against 15 existing path→slug pairs. Use scripts/claude-slug.py.

Four consequences:

• sed 's:/:-:g' is wrong for any path containing ., _, or a space — the common "is the new slug free?" precheck then passes vacuously against a name Claude Code will never read, and the move lands in a dead directory.
• Slugs collide. my_app, my.app, my-app and my/app all produce my-app. An occupied destination slug may belong to a different project — stop and look, never merge blindly.
• A real rename can leave the slug unchanged. my_app → my-app is a genuine move on disk that flattens to the same slug. Then the session dir is already right: change the registry key only, and do not move a directory onto itself.
• Never derive the slug from a transcript's cwd. Verified false on this machine: several worktree slug dirs hold transcripts whose first cwd is the main repo or even a different worktree. Derive from the path, not the file.

Enumerate the slug dirs the repo owns — from real paths, never string prefixes

A repo with git worktrees owns several slug dirs, and they split by location: only worktrees inside the repo change path when the repo moves, so only their slug dirs move. A worktree parked outside the repo keeps its path, so its slug dir must be left exactly where it is — moving it orphans those sessions (it still needs a git repair, since its pointer into the repo changed).

scripts/worktree-slugs.py does this classification, computes each old→new slug, flags an occupied destination, and emits the repair list. Do not hand-roll it from git worktree list text: a line-based pipeline mangles a path containing a newline (verified — it reported a different, truncated path), and splitting on whitespace truncates at a space. The script reads the NUL-terminated -z form.

Do not collect them by prefix-matching slug names: because every separator flattens to -, -a-b-c may be /a/b/c, /a/b-c or /a/b.c. A sibling directory called repo-name-extra is indistinguishable from repo/name/extra, so a prefix sweep can drag in another project's sessions.

Order of operations — inventory → back up → confirm → mutate → verify

1. Inventory read-only. Destination path clear; destination slug(s) clear; session count; worktree list; uncommitted work; the exact set of ~/.claude.json references (keys and values — there is usually more than one).
2. Back up before mutating anything: the whole slug dir, ~/.claude.json, and any uncommitted/untracked work.
3. Confirm the plan with the user — old path, new path, session count, the worktrees affected, and which sibling repos you are not touching.
4. Mutate as one && chain with the repo move LAST. Any earlier failure then aborts while the repo is still where everyone expects it. (rename() keeps the inode, so an open shell's cwd follows the repo.)
5. Verify (below) — and treat a failed check as unfinished work, not noise.

Run this from outside the repo being moved (e.g. from $HOME). Then no session in the slug dir is live, and the move is a clean rename. If you are running inside it, your own session is live in that slug — symlink the old slug name at the new one as a hedge, and never rewrite a transcript that is being appended to.

~/.claude.json is a live file — atomic is not enough

Every running Claude Code process reads and rewrites it. Verified: with 5 claude processes up, the file's mtime was 17 seconds old. A temp-file + os.replace prevents a torn file; it does not prevent a lost update — another session that loaded the JSON before your write will happily save its version over yours.

So: do the registry edit with no other sessions running, and re-check afterwards that your rename survived.

What the entry carries (verified field names): hasTrustDialogAccepted, hasCompletedProjectOnboarding, allowedTools, mcpServers, enabledMcpjsonServers/disabledMcpjsonServers, mcpContextUris, hasClaudeMdExternalIncludesApproved, lastSessionId, plus usage stats.

The old path also appears outside projects — most often as values in githubRepoPaths["<org>/<repo>"], which is a list of local checkout paths. Fix those values; the <org>/<repo> keys are GitHub identifiers, not paths. Same for the git remote: [e-mail]:<org>/<repo>.git may contain the old parent name and must never be rewritten. Only ever replace a full absolute local path, anchored — never a bare folder or org substring.

Use scripts/remap-claude-json.py: it repoints keys and values that are exactly OLD or live under OLD/, refuses on a destination-key collision, refuses to write if any anchored reference would survive, and is dry-run unless --apply.

Git worktrees break — and git worktree repair is the fix

Worktrees store absolute paths in both directions (verified on git 2.43.0):

• <repo>/.git/worktrees/<name>/gitdir → absolute path of the worktree's .git file
• <worktree>/.git → gitdir: <abs path into the repo's .git/worktrees/<name>>

Moving the repo invalidates both, so git commands in the worktree fail. After the move, run git worktree repair from the moved repo, and pass the worktree paths explicitly when the worktrees moved too. Worktrees that live outside the repo (a sandbox/job tmp dir, for example) do not move with it — they still need the repair because the pointer into the repo changed.

Prune first if some are already dead: git worktree prune — but only after confirming nothing uncommitted lives in them.

What not to touch, and why

Path	Why
~/.claude/sessions/<pid>.json	live, pid-scoped; superseded on next launch — editing is racy and pointless
~/.claude/history.jsonl	one global prompt history across all projects; old paths there are cosmetic
~/.claude/file-history/<session-uuid>/…	edit-undo snapshots, session-scoped not project-scoped, so they don't follow the slug dir. Old-path hits here are normal — do not "fix" them
the git remote	a GitHub identifier, not a filesystem path
/tmp/claude-*	ephemeral, recomputed from cwd

Grep the rest of ~/.claude rather than trusting any list of directory names — the layout moves between versions (todos/ is in older runbooks and is absent on 2.1.233). Investigate hits; expect them to be few.

Verify (each check independently — a failed lookup is missing evidence)

• git status --short count and git rev-parse HEAD match the pre-move values.
• The old repo path no longer exists; sibling repos in the old parent are untouched.
• Every expected *.jsonl is present at the new slug, and memory/ came with it.
• ~/.claude.json: new key present, old key gone, hasTrustDialogAccepted still true.
• git worktree list resolves, and a git command inside a worktree succeeds.
• Launch claude from the new path once: the picker lists the old sessions and no trust dialog appears.

Resume is cwd-scoped — claude --resume <uuid> finds a session only from the directory whose slug owns it. Hand the user the new path, not just the uuid.

Rewriting old paths inside transcripts is optional. It only makes stale file:line refs in old scrollback clickable again. Evidence it is unnecessary: a slug dir on this machine was renamed by an earlier migration and its transcripts still carry the pre-move cwd — sessions resume fine. If you do it, only ever touch files no live session is appending to.

Preconditions and portability

• Same filesystem for OLD_REPO and NEW_REPO — that is the move whose atomicity is at stake. (The slug dirs are siblings inside ~/.claude/projects, so that rename is always same-device; the repo-vs-~/.claude comparison is irrelevant.) Across filesystems mv still copies, but open fds won't follow — do it with nothing live in the slug and skip the symlink hedge.
• Every slug starts with -, so ls, mv, cp and rm read a bare slug as a flag. Always use absolute paths, ./, or --.
• mv -T is a GNU coreutils flag (9.4 here) and is the same portability class as the timeout gotcha in this repo's AGENTS.md — on a BSD/macOS mv it fails. The destination-is-clear precheck already rules out the "moved into an existing directory" trap that -T guards, so plain mv is the portable form.
• Needs python3 (3.12 here), git, tar, and write access to ~/.claude.

Environment stamp: facts above were verified on Claude Code 2.1.233, git 2.43.0, GNU coreutils 9.4, Linux. They are compatibility notes about a moving target, not a promise about the machine you are on — re-probe the slug rule and the ~/.claude layout before trusting them.