SciDEX — Task: [Atlas] Build automated gap scanner

## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Completion Notes

Auto-completed by supervisor after successful deploy to main

Git Commits (7)

[Atlas] Update spec work log: gap scanner shim fix [task:f456463e9e67]2026-04-19

[Atlas] Fix gap scanner shim with dynamic paths instead of hardcoded worktree [task:f456463e9e67]2026-04-19

[Atlas] Update spec work log: gap scanner shim fix [task:f456463e9e67]2026-04-19

[Atlas] Fix gap scanner shim with dynamic paths instead of hardcoded worktree [task:f456463e9e67]2026-04-19

[Atlas] Update spec work log: gap scanner shim fix [task:f456463e9e67]2026-04-19

[Atlas] Fix gap scanner shim with dynamic paths instead of hardcoded worktree [task:f456463e9e67]2026-04-19

Squash merge: orchestra/task/f456463e-build-automated-gap-scanner-analyze-new (1 commits)2026-04-17

Spec File

[Atlas] Build automated gap scanner — analyze new papers for contradictions and unknowns

Quest: Gap Factory Priority: P3 Status: open

Goal

Build automated gap scanner — analyze new papers for contradictions and unknowns

Context

This task is part of the Gap Factory quest (Atlas layer). It contributes to the broader goal of building out SciDEX's atlas capabilities.

Acceptance Criteria

☐ Implementation complete and tested

☐ All affected pages load (200 status)

☐ Work visible on the website frontend

☐ No broken links introduced

☐ Code follows existing patterns

Approach

Read relevant source files to understand current state

Plan implementation based on existing architecture

Implement changes

Test affected pages with curl

Commit with descriptive message and push

Work Log

2026-04-17 — Verification

Status: Work already complete on main
Verification: scripts/gap_scanner.py exists on main with full implementation (623 lines)

- Analyzes new papers for contradictions and unknowns using Claude
- Uses landscape context (thin regions, domain whitespace) for targeted gap detection
- Creates knowledge gaps in database when significant gaps found
- Has artifact registry integration for governance/provenance
- Supports dry-run (--review) and execute (--execute) modes
- Commits on main: 41dc07b1b (Senate reorganization), ba9292f41 (dedup governance)

Note: No commits reference task ID f456463e9e67 — work was absorbed into Senate reorganization
Database issue: Pre-existing "malformed database schema" error unrelated to gap scanner code

2026-04-19 — Gap Scanner Shim Fix

Status: Fixed broken backward-compat shim at root gap_scanner.py
Issue: The shim at gap_scanner.py had hardcoded paths to another worktree (task-1f699995ef18) instead of using dynamic paths
Fix: Updated gap_scanner.py to use Path(__file__).resolve().parent for correct relative paths to scripts/deprecated/gap_scanner.py
Verification: python3 gap_scanner.py --help works correctly, script runs and imports modules properly
Commit: 536ae1b22 [Atlas] Fix gap scanner shim with dynamic paths instead of hardcoded worktree [task:f456463e9e67]
Note: Actual implementation is in scripts/deprecated/gap_scanner.py (not scripts/gap_scanner.py as spec originally stated)

Payload JSON

{
  "requirements": {
    "coding": 7,
    "reasoning": 6
  },
  "_reset_note": "This task was reset after a database incident on 2026-04-17.\n\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\ncorruption. Some work done during Apr 16-17 may have been lost.\n\n**Before starting work:**\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\n\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\nSCIDEX_DB_BACKEND=postgres env var.",
  "_reset_at": "2026-04-18T06:29:22.046013+00:00",
  "_reset_from_status": "done"
}