Unlinking an Obsidian vault deletes the shared brain.db (wipes PDF/Tropy/journal indexes too)

[inactinique]

Summary

Clicking "Unlink" on an Obsidian vault does not just remove the vault link — it deletes the entire project's shared .cliodeck/brain.db, which also holds the PDF vector index, the Tropy (primary source) index, and the research journal/history. A user reasonably expects "unlink vault" to be a safe, narrowly-scoped, reversible action; instead it silently wipes unrelated indexed corpora.

Found while auditing the ClioDeck wiki against the actual code (pass 11, brainstorm & integrations cluster).

Current behavior (verified against code)

• obsidianStorePath() (backend/integrations/obsidian/ObsidianVaultIndexer.ts:313-315) returns path.join(workspaceRoot, '.cliodeck', 'brain.db') — the same shared database used elsewhere in the app, not a dedicated Obsidian file.
• backend/core/workspace/layout.ts:67 confirms brainDb: path.join(root, 'brain.db') is the one shared store for PDF vectors, Tropy primary sources, and journal history (consistent with the CLAUDE.md architecture note: ".cliodeck/brain.db — shared SQLite store (PDFs + Tropy + research history)").
• The fusion:vault:unlink IPC handler (src/main/ipc/handlers/fusion-handlers.ts:619-634) does:

  const dbPath = obsidianStorePath(root);
  try {
    await fs.unlink(dbPath);
  } catch {
    // db already gone — fine.
  }

  This deletes brain.db outright, with no check that the file is shared with non-Obsidian data and no backup/confirmation beyond whatever generic UI confirmation (if any) precedes the unlink action.
• This appears to have been introduced by a change (referenced by the auditing agent as commit c044d42) that consolidated the previously-separate obsidian-vectors.db into the shared brain.db — the unlink handler was not updated to account for the new shared-file risk.

Impact

A user unlinking an Obsidian vault (e.g. to switch to a different vault, or because they no longer want Obsidian notes indexed) unknowingly destroys:

• Their entire indexed PDF/bibliography corpus (would need full re-indexing).
• Their indexed Tropy primary-source archive.
• Their AI usage journal / research history.

This is data loss disguised as a narrow, reversible settings change — comparable in shape to already-filed issue #16 (journal purge wipes PDF index), but arguably more severe given how routine "switch vaults" or "remove a vault I no longer use" sounds to a user.

Suggested fix

fusion:vault:unlink should stop deleting brain.db wholesale. Either:

• Scope the deletion to Obsidian-sourced rows/vectors only (requires the store to distinguish source type at the row level), or
• Stop deleting the file at all on unlink — just clear cfg.vault and leave stale Obsidian vectors to be pruned on next re-index (consistent with how other "detach" actions in the app behave, e.g. removing a book chapter from the manifest never touches the file).

Evidence trail

• backend/integrations/obsidian/ObsidianVaultIndexer.ts:313-315 — obsidianStorePath().
• backend/core/workspace/layout.ts:67 — confirms brain.db is the shared store.
• src/main/ipc/handlers/fusion-handlers.ts:619-634 — the unlink handler.
• src/main/services/pdf-service.ts:161, 1.9-Journal-and-History.md ("Research journal (brain.db)") — confirm other subsystems share this same file.
• Wiki page corrected in the same pass: 1.14-Obsidian-Vault-Guide.md.