Troubleshooting

Symptom Action
doctor passes but Zotero fails Start Zotero, enable its local API, and inspect the separate Zotero result.
Metadata imports but no PDF Check ZOTERO_STORAGE_DIR and the linked attachment base separately.
MinerU parse fails A present command does not prove authentication or network readiness; use an isolated copy for a real parse.
Analysis is needs_update Its source fingerprint changed; review and explicitly update it.
Analysis Base is absent Call literature_rebuild_analysis_base.
Client does not show 31 tools Verify the actual package and launch command, restart it, then redo the handshake.
obsidian-vault-mcp doctor --vault-path "<VAULT_PATH>"
obsidian-vault-mcp verify --vault-path "<VAULT_PATH>"
obsidian-vault-mcp preview <transaction-id> --vault-path "<VAULT_PATH>"
obsidian-vault-mcp rollback <transaction-id> --vault-path "<VAULT_PATH>" --dry-run