Troubleshooting

When something is not working right, start with the fast built-in checks and work toward more detailed diagnostics only if you need them.

First step: `nimbus doctor`

nimbus doctor is the quickest health check. Run it any time something feels off — it covers the most common failure modes and tells you exactly what to fix.

nimbus doctor

What it checks:

Bun version — confirms Bun ≥ 1.2 is installed.
Vault — on Linux, verifies secret-tool is on PATH; on Windows and macOS, confirms the OS-native store is reachable.
Voice binaries — if [voice] is enabled in nimbus.toml, checks that whisper-cli (or the configured whisper_path) is on PATH and that the configured Piper binary and model file are present.
Gateway process — checks that the Gateway is running and that the IPC socket is reachable.
Config — calls config.validate to surface any schema errors or warnings in nimbus.toml.
Index — reports the total number of indexed items; warns if the count is zero (meaning the initial sync has not yet completed).
Connector health — lists every registered connector with its current health state.

Representative output:

Runtime: Bun 1.2.14
[ok] Bun version meets minimum.
Data dir: C:\Users\alice\AppData\Local\Nimbus\data
Gateway state file: C:\Users\alice\AppData\Local\Nimbus\data\gateway.json
[ok] Vault: OS-native store (win32) — no Linux secret-tool check.
[ok] Gateway: IPC OK (uptime ~312s).
[ok] Config: valid.
[ok] Index: 48201 items.
Connector health:
  [ok] github: healthy
  [ok] slack: healthy
  [warn] jira: degraded

Exit code 0 = all green. 1 = warnings only. 2 = at least one failure.

Detailed snapshot: `nimbus diag`

nimbus diag captures a full system snapshot. It is the canonical attachment for bug reports.

nimbus diag             # pretty-printed JSON to stdout
nimbus diag --json      # same (explicit flag)

The snapshot includes vault status, active profile, the full connector list with health state and last-sync timestamp, index metrics (item counts, embedding coverage, DB size on disk), and recent errors.

For bug reports:

nimbus diag --json > diag.json

Attach diag.json when filing an issue at github.com/nimbus-agent/Nimbus/issues.

Slow-query log:

nimbus diag slow-queries                   # last 50 queries that exceeded the threshold
nimbus diag slow-queries --limit 20        # top 20
nimbus diag slow-queries --since 24h       # last 24 hours only

The default slow-query threshold is 100 ms. Queries are logged to the query_latency_log table in the index. If you see recurring slow queries, run nimbus db verify next.

Index integrity: `nimbus db verify`

nimbus db verify runs non-destructive checks against the local SQLite index. Nothing is written to the database.

nimbus db verify

Checks performed (in order):

Check	What it tests
`integrity_check`	SQLite page-level corruption (`PRAGMA integrity_check`)
`fts5_consistency`	FTS5 shadow table consistency (the internal `integrity-check` command)
`vec_rowid_mismatch`	`vec_items_384` row count vs `embedding_chunk` row count
`orphaned_sync_tokens`	`sync_state` rows with no matching `scheduler_state` entry
`schema_version`	Latest `_schema_migrations` row vs expected target version
`foreign_key_integrity`	`PRAGMA foreign_key_check`

Exit code 0 = all checks pass. Exit code 1 = at least one finding.

Run nimbus db verify after any unexpected shutdown or if nimbus doctor reports index anomalies.

Repair: `nimbus db repair`

When nimbus db verify reports findings, nimbus db repair runs targeted recovery actions. It will not make destructive changes without explicit confirmation.

nimbus db repair          # shows what would be done, prompts before each action
nimbus db repair --yes    # runs all applicable actions without prompting

Repair actions:

Finding	Action taken
`vec_rowid_mismatch`	Deletes orphaned `vec_items_384` rows; resets affected connector cursors so embeddings re-queue
`fts5_consistency`	Rebuilds the FTS5 index (`INSERT INTO item_fts(item_fts) VALUES('rebuild')`)
`orphaned_sync_tokens`	Deletes `sync_state` rows whose connector is no longer registered
`foreign_key_integrity`	Cascade-deletes rows that violate foreign-key constraints

Every repair action is written to the audit_log table with action = 'db.repair'. You can review repair history with nimbus audit verify.

Snapshots and backups

The Gateway takes automatic pre-migration backups before every schema migration. You can also take and restore manual snapshots:

nimbus db snapshot                  # take a manual snapshot now
nimbus db snapshots list            # list manual snapshots
nimbus db backups list              # list automatic pre-migration backups
nimbus db restore <snapshot-path>   # restore from a snapshot file
nimbus db prune                     # remove old snapshots (prompts before deleting)
nimbus db prune --yes               # prune without prompting

Snapshots live in <dataDir>/snapshots/ and pre-migration backups in <dataDir>/backups/. See Log locations below for the platform-specific dataDir.

Common problems

Symptom	Likely cause	What to try
Gateway won’t start	Port or socket already in use; stale lock file	Run `nimbus stop` to clear the stale state; check for another Nimbus process with `nimbus doctor`
Connector shows `unauthenticated`	OAuth token expired or was revoked	Re-auth via Settings → Connectors → Connect, or `nimbus connector auth <service>`
`nimbus ask` returns “no results”	Indexer hasn’t completed initial sync	Run `nimbus connector list` to see sync state; wait for the first sync to finish or trigger one manually with `nimbus connector sync <service>`
Tauri app banner “Gateway is not running”	Gateway process exited or was not started	Run `nimbus start` from a terminal; or click “Start Gateway” in the banner
Voice doesn’t transcribe	`whisper-cli` not on PATH; or `whisper_path` in `nimbus.toml` points to a missing binary	Run `nimbus doctor` — it checks voice binary paths; update `[voice] whisper_path` if needed
Slow queries accumulate	Large index without FTS5 vacuum; vec alignment drift	Run `nimbus diag slow-queries` to identify culprits; then `nimbus db verify` and `nimbus db repair --yes` if findings are reported
`nimbus connector sync` hangs	Rate-limit or network timeout on the upstream API	Check `nimbus connector list` for `rate_limited` state; wait for backoff to expire; verify connectivity

Log locations

The Gateway writes a structured JSON log file per calendar day. The file basename is gateway-YYYY-MM-DD.log.

Platform	Log directory
Windows	`%LOCALAPPDATA%\Nimbus\data\logs\`
macOS	`~/Library/Application Support/Nimbus/logs/`
Linux	`~/.local/share/nimbus/logs/` (or `$XDG_DATA_HOME/nimbus/logs/` if `XDG_DATA_HOME` is set)

The CLI also writes a per-day log (cli-YYYY-MM-DD.log) to the same directory.

Log lines are newline-delimited JSON (Pino format). To read them in a readable form:

# macOS / Linux
cat "$(nimbus diag --json | jq -r '.logDir')/gateway-$(date +%Y-%m-%d).log" | npx pino-pretty

# Windows PowerShell
Get-Content "$env:LOCALAPPDATA\Nimbus\data\logs\gateway-$(Get-Date -Format 'yyyy-MM-dd').log"

Credential fields (*.token, *.secret, oauth.*) are redacted by the logger before they reach disk — you will see [Redacted] in their place.

WSL note

If you are running Nimbus inside WSL on Windows, the Linux installer places nimbus under ~/.local/bin inside the WSL filesystem. The Windows side (PowerShell, cmd) cannot see that binary unless you also install Nimbus natively on Windows.

The two installations are separate and independent — different Vault, different SQLite index, different nimbus.toml. If you want Nimbus available in both environments you need to install it in both. This is by design: WSL and the Windows host do not share credential stores.

Filing an issue

github.com/nimbus-agent/Nimbus/issues

Include the output of:

nimbus diag --json > diag.json

The JSON snapshot contains vault status, connector health, index metrics, and recent errors — everything needed to diagnose most problems without back-and-forth.

Do not include log files in a public issue unless you have reviewed them for sensitive data; the logger redacts credentials, but your log lines may contain file paths or message previews that you prefer to keep private.

Where to next

FAQ Frequently asked questions about Nimbus.

HITL & safety How Nimbus asks for your approval before any write action.

Verify your download Confirm the binary you downloaded is the genuine release.