> ## Documentation Index
> Fetch the complete documentation index at: https://docs.getgaal.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Pruning orphaned resources

> Remove skills and MCP entries gaal used to manage but no longer does.

Removing an entry from `gaal.yaml` doesn't, by default, delete what gaal previously installed. The leftover files are called **orphans**. `gaal sync --prune` cleans them up.

Pruning is opt-in because the safe default is "leave alone what I didn't author this run." If you removed a skill from `gaal.yaml` by accident, you don't want gaal to delete it before you notice.

## What gets pruned

| Resource                                | Pruned? | Notes                                                                                                       |
| --------------------------------------- | ------- | ----------------------------------------------------------------------------------------------------------- |
| **Skills**                              | Yes     | Skill directories gaal previously installed and that no longer have a matching `skills[]` entry.            |
| **MCP server entries**                  | Yes     | Inside each managed target file, `mcpServers` keys gaal previously upserted that are no longer in `mcps[]`. |
| **Repositories**                        | No      | gaal never deletes repository directories. Remove them by hand if you want them gone.                       |
| **Other JSON keys in MCP target files** | No      | `--prune` only touches keys gaal could have authored.                                                       |

## Always preview a prune

```bash theme={"theme":"nord"}
gaal sync --prune --dry-run
```

The plan marks pruned items with `-`:

```text theme={"theme":"nord"}
plan:
  skills
    - remove  old-reviewer        ← claude-code (was managed by gaal)
  mcps
    - remove  legacy-server       ← ~/.claude.json
```

## Apply the prune

```bash theme={"theme":"nord"}
gaal sync --prune
```

## Incompatible with `--service`

```bash theme={"theme":"nord"}
$ gaal sync --service --prune
error: --prune and --service are incompatible: use one-shot mode for destructive operations
```

Destructive operations don't belong in an unattended loop. Run prune as a one-shot after editing `gaal.yaml`.

## How gaal knows what it managed

gaal records what it installed each cycle. A skill or MCP entry is considered gaal-managed if a previous sync wrote it. When you remove it from `gaal.yaml` and run `--prune`, that record is what authorises the deletion.

If you delete the gaal state file by hand, gaal forgets what it managed and `--prune` becomes a no-op until you sync again.

## Related

<CardGroup cols={2}>
  <Card title="Dry-run" icon="eye" href="/workflows/dry-run" />

  <Card title="gaal sync" icon="arrows-rotate" href="/cli/sync" />

  <Card title="MCP servers" icon="plug" href="/concepts/mcp-servers" />
</CardGroup>