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Fabro checkpoints every workflow run using Git plus the durable run store. After each node completes, Fabro commits the file changes and execution state so that interrupted runs can be resumed exactly where they left off. This happens automatically — no configuration required beyond running inside a Git repository.

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Two branches, two purposes

Each run creates two Git branches that work in tandem:
BranchRef formatContains
Run branchfabro/run/{run_id}File changes made by agents and commands — the actual work product
Metadata branchfabro/meta/{run_id}Checkpoint JSON, the workflow graph, run and start records, and offloaded artifacts
The run branch is a regular Git branch that grows one commit per completed node. The metadata branch is an orphan branch (no shared history with your code) that stores structured data using Git’s object database directly — no working tree needed.

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Run branch commits

After each node finishes, Fabro stages file changes and creates a commit on the run branch. Files matching [checkpoint] exclude_globs patterns (configured in run.toml or settings.toml) are excluded from staging: 
fabro(01JKXYZ...): plan (success)

Fabro-Run: 01JKXYZ...
Fabro-Completed: 2
Fabro-Checkpoint: a1b2c3d4...
The commit message follows a structured format:
PartDescription
Subject linefabro({run_id}): {node_id} ({status})
Fabro-Run trailerThe run ID
Fabro-Completed trailerNumber of completed nodes so far
Fabro-Checkpoint trailerSHA of the corresponding commit on the metadata branch
The Fabro-Checkpoint trailer links each run branch commit to its metadata branch commit, so you can navigate from file changes to the full execution state and back. Fabro disables Git commit and tag signing for checkpoint commits created inside a sandbox. Your personal or repository-level signing settings can stay enabled, but sandbox bookkeeping does not need access to your signing key.

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Metadata branch

The metadata branch (fabro/meta/{run_id}) is an orphan branch that stores structured run data using Git’s object storage directly (via git2). It is initialized at run start with:
  • run.json — Current projection snapshot: run spec, start/status records, current checkpoint, conclusion, sandbox, retro state, and other run-level metadata
  • graph.fabro — Workflow source for the run
After each node, the metadata branch is updated with:
  • run.json — Refreshed projection snapshot with the new current checkpoint
  • stages/{node_id}@{visit}/... — Per-stage execution trace files (prompts, responses, status, diffs, stdout/stderr, and tool metadata)
  • stages/retro/*.md — Retro prompt/response text when present

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What’s in a checkpoint

The run.json.checkpoint snapshot captures everything needed to resume a run:
FieldDescription
timestampWhen the checkpoint was created
current_nodeThe node that just completed
next_node_idThe next node the engine would execute
completed_nodesOrdered list of all completed node IDs
node_retriesHow many retry attempts each node has used
node_outcomesFull outcome (status, context updates, usage) for each completed node
context_valuesSnapshot of the entire run context
git_commit_shaSHA of the run branch commit at this checkpoint
loop_failure_signaturesFailure signature counts for loop detection
restart_failure_signaturesFailure signature counts across loop-restart edges
The durable run store also keeps the current checkpoint so resume, inspect, and API reads do not need to rely on scratch files.

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Worktrees

Fabro uses Git worktrees to isolate workflow runs from your working directory. When a run starts in a clean Git repository:
  1. Fabro records the current HEAD as the base SHA
  2. Creates a new branch fabro/run/{run_id} at that SHA
  3. Adds a worktree at {run_dir}/worktree on that branch
  4. Changes into the worktree directory for the duration of the run
This means your original working directory stays untouched while the agent makes changes in the worktree. When the run completes, Fabro removes the worktree and restores your original directory.
If the working directory has uncommitted changes, Fabro skips worktree setup and runs in place, logging a warning. Git checkpointing is disabled in this case.
For Daytona sandboxes, the worktree is created inside the remote sandbox instead. The metadata branch is still written to the host repository so that runs can be resumed locally. Both the run branch and the metadata branch are pushed to origin after each checkpoint — the run branch is pushed from the sandbox, while the metadata branch is pushed from the host using a GitHub App installation token.

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Resuming a run

Resume an interrupted run from its durable checkpoint: 
fabro resume 01JKXYZ
Fabro resolves the run by ID prefix, validates that durable state contains a checkpoint, and asks the server to continue execution. No workflow file or override flags are needed — all configuration is restored from persisted state.
  1. Fabro looks up the run directory by ID prefix
  2. Validates that a checkpoint exists in durable state and no engine process is already running
  3. Cleans stale local artifacts from the previous execution
  4. Resets status to Submitted and spawns a new engine subprocess with --resume
  5. The engine restores the full context, completed node list, retry counts, and failure signatures from durable state
  6. If the checkpointed node used full fidelity, downgrades the first resumed node to summary:high (since the original conversation thread no longer exists in memory)
  7. Continues execution from next_node_id

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The checkpoint cycle

Here’s the full sequence that runs after every node completes:
  1. Append checkpoint event — Persist the new checkpoint into durable run state
  2. Write metadata branch — Serialize the checkpoint and any new artifacts to the metadata branch (shadow commit)
  3. Commit to run branch — Stage all file changes, commit with structured trailers linking to the shadow commit SHA
  4. Update durable checkpoint — Persist the git_commit_sha associated with the run-branch commit
Steps 2-4 are best-effort — if any Git operation fails, the run continues and emits a RunNotice warning event. Resume still uses the durable checkpoint in the run store.

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Inspecting run history

Because checkpoints are plain Git commits, you can inspect them with standard Git tools: 
# View the commit log for a run
git log fabro/run/01JKXYZ... --oneline

# See what an agent changed at a specific node
git show fabro/run/01JKXYZ...

# Diff the full run against the starting point
git diff main..fabro/run/01JKXYZ...

# Read checkpoint data from the metadata branch
git show fabro/meta/01JKXYZ...:run.json | jq .checkpoint.current_node

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Rewinding to an earlier checkpoint

If a later stage goes off-track, you can rewind a terminal run to an earlier checkpoint and resume from there instead of restarting the entire workflow. Rewind creates a replacement run at the target checkpoint, archives the source run, and prints the new run ID to resume: 
# List the checkpoint timeline
fabro rewind <RUN_ID> --list

# Rewind to a specific checkpoint
fabro rewind <RUN_ID> plan@2

# Resume from the rewound point
fabro resume <NEW_RUN_ID>
The source run must already be terminal (succeeded, failed, or dead). If the source is archived, unarchive it first. If archive fails after the replacement run is created, do not retry fabro rewind; archive the source run manually. See fabro rewind for the full command reference.

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Forking a run

If you want to explore an alternate path from a checkpoint without archiving the original run, use fabro fork instead of fabro rewind. Fork creates a new independent run branching from the target checkpoint; the original run stays intact. 
# List checkpoints
fabro fork <RUN_ID> --list

# Fork from a specific checkpoint
fabro fork <RUN_ID> plan@2

# Resume the forked run
fabro resume <NEW_RUN_ID>
Use rewind when a terminal run should be abandoned and replaced from an earlier point. Use fork when you want to try a different approach while keeping the original run as a reference. fabro rewind --list, fabro fork --list, fabro rewind, and fabro fork are server-backed. The server must be able to read the run’s recorded working_directory; otherwise these commands fail. Timeline listing reads the metadata branch as-is and does not rebuild a missing metadata branch, so a missing branch appears as an empty timeline. See fabro fork for the full command reference.

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When checkpointing is active

Git checkpointing activates automatically when:
  • The working directory is a clean Git repository (local and Docker sandboxes)
  • The sandbox is Daytona (metadata branch on the host, commits inside the sandbox)
It is skipped when:
  • The working directory has uncommitted changes
  • The working directory is not a Git repository
  • The run uses --dry-run