feat(doctor): add operational diagnostics and repair#287
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Alan-TheGentleman merged 2 commits intomainfrom Apr 30, 2026
Merged
feat(doctor): add operational diagnostics and repair#287Alan-TheGentleman merged 2 commits intomainfrom
Alan-TheGentleman merged 2 commits intomainfrom
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Pull request overview
Adds a new operational “doctor” surface to Engram for read-only diagnostics (CLI + MCP parity), plus a narrowly-scoped, backup-gated doctor repair flow to reclassify project-contaminated session data.
Changes:
- Introduces
internal/diagnosticrunner/registry + MVP checks and wires them intoengram doctorand MCPmem_doctor. - Adds
engram doctor repairplan/dry-run/apply workflow with a diagnostic-based planner and store-owned backup + session-scoped project reclassification. - Adds documentation and OpenSpec artifacts (design/spec/tasks/verification/manual verification) for diagnostics and repair.
Reviewed changes
Copilot reviewed 33 out of 33 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
cmd/engram/main.go |
Wires doctor into CLI dispatch and adds a shared runDiagnostics adapter. |
cmd/engram/doctor.go |
Implements engram doctor (text/JSON) and engram doctor repair (plan/dry-run/apply) CLI flows. |
cmd/engram/doctor_test.go |
Adds CLI tests for diagnostics, MCP parity, and repair validation/JSON/apply behavior. |
internal/diagnostic/diagnostic.go |
Adds core diagnostic types, report envelope, runner, and error report helper. |
internal/diagnostic/registry.go |
Adds deterministic check registry + invalid-check error handling. |
internal/diagnostic/checks.go |
Implements MVP checks (directory mismatch, manual session mismatch, mutation required fields, SQLite lock contention). |
internal/diagnostic/diagnostic_test.go |
Adds unit tests for runner/registry and check branches (incl. deterministic lock contention seam). |
internal/diagnostic/repair.go |
Adds repair planning for supported mismatch checks into deterministic action lists. |
internal/diagnostic/repair_test.go |
Adds unit tests for repair planning rules (trusted evidence, manual naming constraints, skip reasons). |
internal/store/diagnostic.go |
Adds store read helpers for diagnostics plus backup + apply/estimate APIs for session-scoped reclassification. |
internal/store/diagnostic_repair_test.go |
Adds store tests for estimate non-mutation and apply safety boundaries (backup + allowed tables only). |
internal/store/store_test.go |
Adds tests for new diagnostic read helpers and lock snapshot non-mutation. |
internal/mcp/mcp.go |
Registers mem_doctor tool (agent profile) and handler using the shared diagnostic runner. |
internal/mcp/mcp_test.go |
Updates tool allowlists/count expectations and adds mem_doctor contract tests (auto-detect, unknown project, envelope shape). |
docs/DOCTOR.md |
Documents doctor/repair CLI forms, MCP contract, check catalog, safety boundaries, and clone-safe workflow. |
openspec/changes/doctor-diagnostic/spec.md |
Points root spec note to canonical spec deltas to avoid conflicting requirements. |
openspec/changes/doctor-diagnostic/proposal.md |
Captures intent/scope/approach/risks for the diagnostic feature. |
openspec/changes/doctor-diagnostic/design.md |
Documents architecture decisions and contracts for diagnostic runner/CLI/MCP. |
openspec/changes/doctor-diagnostic/exploration.md |
Records exploration context and rationale for the approach. |
openspec/changes/doctor-diagnostic/tasks.md |
Tracks implementation tasks/phases for diagnostics. |
openspec/changes/doctor-diagnostic/manual-verification.md |
Adds manual verification matrix + clone walkthrough evidence. |
openspec/changes/doctor-diagnostic/apply-progress.md |
Records apply progress and verification gap fixes for diagnostics. |
openspec/changes/doctor-diagnostic/verify-report.md |
Adds verification report for diagnostics (tests, docs alignment, evidence mapping). |
openspec/changes/doctor-diagnostic/specs/operational-diagnostics/spec.md |
Defines canonical diagnostic requirements and scenarios. |
openspec/changes/doctor-diagnostic/specs/mcp-project-resolution/spec.md |
Extends MCP read-tool optional project requirement to include mem_doctor. |
openspec/changes/doctor-repair-reclassify-project/proposal.md |
Captures intent/scope/approach/risks for repair MVP. |
openspec/changes/doctor-repair-reclassify-project/design.md |
Documents repair architecture, interfaces, and testing strategy. |
openspec/changes/doctor-repair-reclassify-project/exploration.md |
Records exploration context and repair design implications. |
openspec/changes/doctor-repair-reclassify-project/tasks.md |
Tracks implementation tasks/phases for repair. |
openspec/changes/doctor-repair-reclassify-project/manual-verification.md |
Documents clone-safe manual verification commands and observed outputs. |
openspec/changes/doctor-repair-reclassify-project/apply-progress.md |
Records apply progress and verification notes for repair MVP. |
openspec/changes/doctor-repair-reclassify-project/verify-report.md |
Adds verification report for repair MVP (requirements mapping + evidence). |
openspec/changes/doctor-repair-reclassify-project/specs/operational-diagnostics/spec.md |
Defines repair-related requirement deltas and scenarios. |
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Comment on lines
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| if err != nil { | ||
| report = diagnostic.ErrorReport(project, err) | ||
| if jsonOut { | ||
| writeDoctorJSON(report) | ||
| } else { |
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| } | ||
| nameProject := normalizeProjectName(strings.TrimPrefix(session.Name, "manual-save-")) | ||
| sessionProject := normalizeProjectName(session.Project) | ||
| if nameProject == "" || sessionProject == "" || nameProject == sessionProject || !knownProjects[nameProject] { | ||
| continue |
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| ### Requirement: REQ-OD-005 MVP Non-Repair Constraint | ||
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| The doctor MVP MUST NOT perform repair, apply, or write transactions. `requires_confirmation` MUST be false for all MVP checks because no apply path exists. | ||
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Alan-TheGentleman
changed the base branch from
feat/memory-conflict-surfacing-cloud-sync
to
main
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🔗 Linked Issue
Closes #286
🏷️ PR Type
type:bug— Bug fixtype:feature— New featuretype:docs— Documentation onlytype:refactor— Code refactoring (no behavior change)type:chore— Maintenance, dependencies, toolingtype:breaking-change— Breaking change📝 Summary
engram doctorread-only operational diagnostics with CLI JSON/text output and MCPmem_doctorparity.engram doctor repairplan/dry-run/apply flows for session-scoped project reclassification with backup-before-apply safety.sias-appcontamination shape.📂 Changes
cmd/engram/doctor.gointernal/diagnostic/internal/store/diagnostic.gointernal/mcp/mcp.gomem_doctoras a read-only agent tool.docs/DOCTOR.mdopenspec/changes/doctor-*🧪 Test Plan
go test ./...go test -tags e2e ./internal/server/...Manual testing:
.backupclones only; production~/.engram/engram.dbwas not mutated.--planand--dry-runare non-mutating.--applycreates a backup and updates onlysessions.project,observations.project, anduser_prompts.project.engram doctor --json --project sias-appreturned OK in the repaired clone.🤖 Automated Checks
Closes #N/Fixes #N/Resolves #Nstatus:approvedlabeltype:*labelgo test ./...passesgo test -tags e2e ./internal/server/...passes✅ Contributor Checklist
Closes #N)type:*label to this PRgo test ./...go test -tags e2e ./internal/server/...Co-Authored-Bytrailers in commits💬 Notes for Reviewers
This is a stacked PR based on
feat/memory-conflict-surfacing-cloud-syncso the review diff stays scoped to the doctor work instead of reintroducing the prior memory-conflict/cloud-sync branch history.