doctor - Entire

Diagnose problems in the current repository and offer to fix them.

entire doctor [flags]

Flag	Description
`-f, --force`	Fix all issues without prompting (condense if possible, otherwise discard)

What Doctor Checks

Check	What it reports
Disconnected metadata branches	The local and remote `entire/checkpoints/v1` branches share no common ancestor. Doctor fixes this by cherry-picking local checkpoints onto the remote tip.
Operational logs	Entire cannot write to `.entire/logs`, so diagnostics may be missing.
Codex hook trust	Installed Codex hooks lack a `trusted_hash` entry in your Codex config. Review and approve them with `/hooks` in Codex.
Hook config drift	Installed agent hooks differ from the current CLI configuration. Run `entire enable --force` to reinstall them.
Stuck sessions	See Stuck Sessions below.

Stuck Sessions

A session is considered stuck if:

It is in ACTIVE phase with no interaction for over 1 hour
It is in ENDED phase with uncondensed checkpoint data on a shadow branch

For each stuck session, you can choose to:

Condense: Save session data to permanent checkpoint storage
Discard: Remove the session state and shadow branch data
Skip: Leave the session as-is

Without a terminal to prompt on, such as an agent or CI, entire doctor reports each issue and points at --force instead of prompting.

doctor migrate-checkpoints

Convert the checkpoints on the entire/checkpoints/v1 branch into per-checkpoint refs under refs/entire/checkpoints/<shard>/<id>, the layout the ref-based backend uses.

entire doctor migrate-checkpoints [flags]

Flag	Description
`--dry-run`	Report what would be migrated without writing refs
`--remote NAME`	Remote to push migrated refs to. Defaults to the checkpoint sync remote

Each checkpoint keeps its 12-character hex ID as the ref name, and its current tree is wrapped in a fresh commit. The command does not remap the existing branch commits and does not delete the branch. It skips checkpoints it has already converted, so re-running it after more branch activity is safe. Run it while the branch backend is still primary. Once checkpoints.primary.type is git-refs, the command reports that there is nothing to migrate and exits, because the refs are authoritative at that point. New refs are queued for push. Run interactively, the command asks whether to push them now. Run without a terminal, it leaves them queued, and they flush on the next git push once the ref-based backend is primary.

Migration is optional. See Both Backends Stay Readable for how readers resolve branch-backed checkpoints after a switch.

doctor logs

Show recent operational logs.

entire doctor logs [flags]

Flag	Description
`-f, --follow`	Stream new log lines as they are written
`--tail N`	Show the last N lines. Use `0` for all. Defaults to `100`.

doctor bundle

Produce a diagnostic bundle for bug reports.

entire doctor bundle [flags]

Flag	Description
`-o, --out PATH`	Path to write the bundle archive. Defaults to the OS temp directory.
`--raw`	Skip secret redaction. Use only when support has asked for an unredacted bundle.

doctor trace

Show hook performance traces for debugging slow Git operations.

entire doctor trace [flags]

Flag	Description
`--hook TYPE`	Filter by hook type, such as `post-commit`, `prepare-commit-msg`, or `pre-push`
`--json`	Output as JSON
`--last N`	Show the last N hook invocations. Defaults to `1`.
`--slow`	Only include traces flagged slow, meaning those logged at WARN
`--summary`	Aggregate across traces instead of showing each one, reporting which step dominates per hook. Uses `--last 200` unless you set `--last`.

# The most recent hook trace
entire doctor trace

# The last five post-commit traces
entire doctor trace --last 5 --hook post-commit

# Which step dominates, across the slow traces only
entire doctor trace --summary --slow

Hooks that take 1.5 seconds or longer are traced by default, at WARN level, so a slow hook records its own breakdown with no configuration. Set ENTIRE_PERF_SLOW_MS=0 to turn that off. A log_level above WARN also hides them.

To trace every hook, including fast ones, raise verbosity: set ENTIRE_LOG_LEVEL=DEBUG in your shell profile, or add "log_level": "DEBUG" to .entire/settings.json.

​What Doctor Checks

​Stuck Sessions

​doctor migrate-checkpoints

​doctor logs

​doctor bundle

​doctor trace

What Doctor Checks

Stuck Sessions

doctor migrate-checkpoints

doctor logs

doctor bundle

doctor trace