feat(optimize-sorting): unified optimize-sorting workflow with CLI wiring and three fixes

[colehurwitz]

Combines PRs #1430, #1433, #1435, #1442 into a single PR.

What this adds

Workflow (.factory/workflows/optimize_sorting.py)

Three-tier iterative speed optimization for spike sorting pipelines:

• Tier 1: Config sweep (parameter tuning, zero code changes)
• Tier 2: Code optimization (preserve algorithmic behavior)
• Tier 3: Algorithm changes (strict 0.5% overall + 5% per-unit gates)

CLI wiring

• Added optimize-sorting to CEO_MODES
• Added mode suffix for task builder
• Focus.txt routing for tier selection
• WORKFLOW_META entry for SKILL generation
• --focus allowlist support

Three fixes from #1442

1. Standardized experiment storage (.factory/experiments/optimize-sorting.jsonl)
2. Added to --focus mode allowlist
3. Code-change attribution with 2σ variance detection in PR comments

Tests and docs

• tests/test_optimize_sorting_workflow.py (61 tests, all passing)
• workflow-optimize-sorting/SKILL.md (auto-generated)

Supersedes #1430, #1433, #1435, #1442

[github-actions]

Sentrux Quality Report

Absolute

Scanning ....
[scan] git ls-files: 629 total, 615 kept, 14 dropped (ext:14, meta:0, big:0)
[build_project_map] 615 files, 111 unique dirs, 102 cache misses, 5.4ms
[resolve] 1154 resolved, 1573 unresolved (of 2727 total specs)
[resolve_imports] project_map 5.5ms, suffix_idx 1.5ms, suffix_resolve 18.8ms, total 25.8ms
[build_graphs] 615 files | maps 2.0ms, imports 26.0ms, calls+inherit 6.5ms, total 34.4ms | 1153 import, 8373 call, 1 inherit edges
sentrux check — 3 rules checked

Quality: 4449

✗ [Error] max_cc: 5 function(s) exceed max cyclomatic complexity of 30
    factory/cli/_ceo_helpers.py:_execute_ceo (cc=46)
    factory/cli/_ceo_helpers.py:_validate_ceo_flags (cc=43)
    examples/chess_evolve.py:main (cc=33)
    factory/cli/_task_builder.py:_build_ceo_task (cc=32)
    factory/outer_loop/mutations.py:validate_and_repair (cc=31)

✗ 1 violation(s) found

Diff (vs base branch)

Scanning ....
[scan] git ls-files: 629 total, 615 kept, 14 dropped (ext:14, meta:0, big:0)
[build_project_map] 615 files, 111 unique dirs, 102 cache misses, 5.6ms
[resolve] 1154 resolved, 1573 unresolved (of 2727 total specs)
[resolve_imports] project_map 5.7ms, suffix_idx 1.1ms, suffix_resolve 19.8ms, total 26.6ms
[build_graphs] 615 files | maps 2.3ms, imports 26.7ms, calls+inherit 6.2ms, total 35.2ms | 1153 import, 8373 call, 1 inherit edges
sentrux gate — structural regression check

Quality:      4449 -> 4449
Coupling:     0.80 → 0.80
Cycles:       4 → 4
God files:    2 → 2

Distance from Main Sequence: 0.35

✗ DEGRADED
  ✗ Complex functions increased: 67 → 68