# Reported issues for Rhizome MCP Pod holds 5 of 5 GitHub reports that passed its relevance review. This can include external user reports, maintainer-confirmed bugs, and concrete feature gaps. Treat them as evidence to inspect, not a count of distinct defects. Back to [Rhizome MCP](/mcp/rhizome-mcp). ## Most discussed ### Feature request: identify which repository an orphaned project database belongs to after the repository is deleted ## Summary This report requests a supported way, in the CLI or the MCP server, to identify which repository a rhizome-mcp project database under the data root belonged to after that repository has been deleted, and, optionally, the recording of the initializing repository path so future orphans are self-describing. ## Why this matters - Sooner or later every data root gets cleaned up: disk pressure, a new machine, or plain tidying eventually forces a decision about each orphan, and today… [Read the thread](https://github.com/Odrin/rhizome-mcp/issues/12) · 2026-09-05 · closed · external user · 1 comment ### `projects list` copies every stored database in full to temporary storage before inspection, so the listing can fail under the disk pressure it exists to relieve, and temp exhaustion is misreported as a locked database ## Summary `rhizome-mcp projects list`, introduced by [merged PR #13](https://github.com/Odrin/rhizome-mcp/pull/13) and released in rhizome-mcp 1.5.0, unconditionally copies every database it inspects in full (main file plus `tasks.db-wal` and `tasks.db-shm` sidecars) into a temporary directory before any inspection outcome is determined. The copy happens even when inspection cannot succeed, and the temporary space required is proportional to the largest database in the data root. Measured on… [Read the thread](https://github.com/Odrin/rhizome-mcp/issues/16) · 2026-09-10 · open · external user · 0 comments ### Opening a stored project by project_ref refuses older schema versions with STORAGE_MIGRATION while the same database migrates automatically through the marker path, and the error names no remedy ## Summary rhizome-mcp has two project-open paths with divergent migration behavior. A routed open by `project_ref` (the MCP `get_project` and `open_project` tools with an explicit `project_ref`, and every project-scoped tool call routed through it) refuses to open a database whose schema version is older than the binary's, failing with a non-retryable `STORAGE_MIGRATION` error: `project database schema version is out of date`. The marker-based open of the very same database runs… [Read the thread](https://github.com/Odrin/rhizome-mcp/issues/15) · 2026-09-10 · open · external user · 0 comments ### `projects list` can report a project state that never existed when the database changes during the listing ## Summary `rhizome-mcp projects list`, introduced by [merged PR #13](https://github.com/Odrin/rhizome-mcp/pull/13) and released in rhizome-mcp 1.5.0, copies each project's `tasks.db`, `tasks.db-wal` and `tasks.db-shm` sequentially into a temporary directory with no SQLite coordination, so a commit or `wal_checkpoint` running concurrently with the listing can leave the copied main file mixing pages from before and after that write. The tool then reports such a mixed state with `status: "ok"`.… [Read the thread](https://github.com/Odrin/rhizome-mcp/issues/14) · 2026-09-10 · open · external user · 0 comments ### Feature request: unarchive_issue, a recovery path for accidental or mistaken archival Archival is the only lifecycle operation in rhizome-mcp with no recovery path. There is no unarchive tool in the [43-tool catalog](https://github.com/Odrin/rhizome-mcp/blob/7ce869fe6aec8fc20a9cc5719f1b95ed622ce320/docs/03-mcp-tools.md#L172-L174), no CLI escape hatch, and no documented way to return an archived issue to normal visibility. One stray archive call, a mis-scoped bulk script, an idempotency-replayed batch, or a wrong issue_id permanently freezes the issue: it vanishes from default… [Read the thread](https://github.com/Odrin/rhizome-mcp/issues/11) · 2026-09-05 · closed · external user · 0 comments ## Most recent The remaining reports are on [the project's issue tracker](https://github.com/Odrin/rhizome-mcp/issues).