brain-doctor

Brain Doctor

Scan the whole graph for the format mistakes that silently corrupt a Logseq graph — inline code wrapped in {{ }} (broken macros), bare #number/hex tags and un-namespaced [[links]] (phantom empty pages), [[file://]] links, and junk/description links — plus data-quality checks — malformed properties, broken/duplicate entries, and missing-structure gaps (see the full catalog in skills/_shared/hygiene-rules.md) — then report them and, on confirmation, repair them. This is a maintenance tool: run it on demand, not as part of the save/load cycle.

See skills/_shared/hygiene-rules.md for the full catalog: each rule with its detection pattern, auto-fixable tier, and remediation. The compose-time rules these checks enforce live in skills/_shared/logseq-format.md.

Modes

• Report (default, "lint brain" / "check brain health" / "why are there empty pages"): detect and summarize, change nothing.
• Fix ("fix brain" / "clean up brain" / explicit "yes, fix them" after a report): repair after a backup, with the user's confirmation.

If the trigger is ambiguous, run Report first and offer to fix.

Prerequisites

Resolve the graph path per skills/_shared/path-resolution.md.

Process

1. Scan. For each rule in skills/_shared/hygiene-rules.md with enforced-at: scan (all 9), run its detection across pages/ and journals/. Collect counts and 1–2 example locations per rule. Stay read-only in this phase.

2. Report. Present a compact health summary grouped by the rule's auto-fixable field:

   • Auto-fixable (yes / safe-only): code-in-braces, bare-hash-tag, unnamespaced-link, file-link, malformed-property (safe tiers only).
   • Needs your call (report): description-link, broken-link (with suggested matches), duplicate-entry (the duplicate groups), structural-integrity (missing props / stub sections). Example:

   Brain health: 12 issues across 6 pages
   Auto-fixable (5):  3 {{code}}, 1 bare #tag, 1 malformed property
   Needs your call (7): 2 broken links (1 likely typo → suggests [[Tasks/CRMGM-1982]]),
                        3 duplicate Session Log entries, 2 pages missing last-updated::
   

   If the graph is clean, say so and stop — no backup, journey-log just ran brain-doctor (clean).

3. Confirm before any write. Never repair without explicit user confirmation — consistent with the plugin's "never persist without confirmation" rule. Ask which classes to fix if the user hasn't said.

4. Back up first. The graph is usually not git-tracked, so there is no undo. Before the first edit, copy pages/, journals/, and logseq/ to a timestamped backup folder (e.g. <graph>/.brain-doctor-backup-<yyyy-MM-dd-HHmm>/ or the host scratchpad). Tell the user where it is. If the backup fails, stop — do not edit.

5. Repair. Apply per auto-fixable:

   • Auto-fixable group: on one confirmation, apply the remediation from skills/_shared/hygiene-rules.md. For high-volume mechanical classes (code-in-braces, bare-hash-tag) a single scripted pass over the affected files is appropriate — this is one-time maintenance, not the per-session surgical save path, and a backup was taken. For malformed-property, auto-fix only the page-top property block; report inline key: value hits for user approval (an inline line may be prose). Hand-fix the brace/backtick edge cases noted in the catalog.
   • Needs-your-call group: walk each finding with the user (per-item or batch), applying only what they approve. Never auto-write broken-link, duplicate-entry, or structural-integrity changes.

6. Verify. Re-run the detections. Confirm zero remaining (excluding intentional forward-references the user chose to keep) and that backtick counts per file are even (no broken inline-code spans).

7. Report results and write a journey-log entry per skills/_shared/journey-log.md with activity line: ran brain-doctor · fixed <N> issues (or ran brain-doctor (clean)).

Important Notes

• Report before repair, backup before write, confirm before both. A graph is the user's long-term memory; never mutate it silently.
• A link to a missing page is not always a bug. Users legitimately reference tickets/pages that don't exist yet. Surface these but default to leaving them unless the user says otherwise.
• Logseq may be running. Recommend the user close Logseq (or pause Sync) during a bulk fix to avoid mid-write sync conflicts.
• Prevention beats cure. When you finish, remind the user that brain-save now follows the compose-time invariants (skills/_shared/logseq-format.md), so a freshly maintained graph should stay clean.