SciDEX — Task: [Atlas] Create background gap-generation agent tha

## 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 (2)

[Atlas] Update spec work log — audit reopen fix2026-04-18

[Atlas] Fix gap scanner service paths to match new locations2026-04-18

Spec File

[Atlas] Create background gap-generation agent that runs continuously

Quest: Gap Factory Priority: P3 Status: completed

Goal

Create background gap-generation agent that runs continuously

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

2026-04-18 17:15 PT — Slot 66 (Audit Reopen)

Audit flagged NO_COMMITS — verifying task was actually done
Found: background gap generation infrastructure exists on main
BUT: scidex-gap-scanner.service references old root paths for gap_scanner.py and gap_pipeline.py
gap_scanner.py moved to scripts/deprecated/gap_scanner.py (Senate cleanup b4a034242)
gap_pipeline.py moved to scidex/agora/gap_pipeline.py (Senate cleanup)
Fixed service ExecStart paths and added backward-compat shim at root
Evidence: git log --grep='1f699995' showed no commits on branch; HEAD == origin/main
Commit: e5c00094e [Atlas] Fix gap scanner service paths to match new locations [task:1f699995ef18]