feat: builder-only seed + mixed lv1/lv2 calibration for outer loop evolution

[akashgit]

Closes #1274

Changes

• Builder-only seed workflow: Added create_seed_workflow(minimal=True) — single-node workflow (just builder, no researcher/health_checker/gate). Gives evolution room to discover mutations.

• Calibration findings:

  • lv1: Both 4-node and builder-only seeds score 100% — zero variance
  • lv2: Builder-only scores 0% — too hard for any workflow variant
  • Mixed lv1+lv2: 57% seed score with meaningful variance

• Key insight: Designer's 3-node variant (researcher→builder→health_checker) scores identical to builder-only (0.571). Prompt quality > graph structure.

• Evolution in progress with mixed calibration (budget=20, 2 generations)

Files

• factory/outer_loop/harbor_evaluator.py — create_seed_workflow(minimal=True) + _create_builder_only_seed()
• scripts/run_evolution.py — CLI args for --minimal, --generations, etc
• scripts/run_calibration_v2.py — lv1 builder-only calibration
• scripts/run_calibration_lv2.py — lv2 builder-only calibration
• scripts/run_evolution_mixed.py — mixed lv1+lv2 evolution runner
• scripts/generate_report.py — multi-level report generator
• results/outer_loop_v2_report.md — comprehensive report

[github-actions]

Sentrux Quality Report

Absolute

Scanning ....
[scan] git ls-files: 661 total, 649 kept, 12 dropped (ext:12, meta:0, big:0)
[build_project_map] 649 files, 107 unique dirs, 98 cache misses, 5.3ms
[resolve] 1252 resolved, 1671 unresolved (of 2923 total specs)
[resolve_imports] project_map 5.4ms, suffix_idx 1.2ms, suffix_resolve 19.8ms, total 26.4ms
[build_graphs] 649 files | maps 2.5ms, imports 26.7ms, calls+inherit 7.2ms, total 36.4ms | 1251 import, 9797 call, 11 inherit edges
sentrux check — 3 rules checked

Quality: 4700

✗ [Error] max_cc: 3 function(s) exceed max cyclomatic complexity of 30
    factory/cli/_ceo_helpers.py:_validate_ceo_flags (cc=43)
    factory/cli/_ceo_helpers.py:_execute_ceo (cc=43)
    factory/cli/run.py:cmd_run (cc=32)

✗ 1 violation(s) found

Diff (vs base branch)

Scanning ....
[scan] git ls-files: 661 total, 649 kept, 12 dropped (ext:12, meta:0, big:0)
[build_project_map] 649 files, 107 unique dirs, 98 cache misses, 5.6ms
[resolve] 1252 resolved, 1671 unresolved (of 2923 total specs)
[resolve_imports] project_map 5.8ms, suffix_idx 1.2ms, suffix_resolve 19.8ms, total 26.8ms
[build_graphs] 649 files | maps 2.4ms, imports 27.0ms, calls+inherit 7.5ms, total 36.9ms | 1251 import, 9797 call, 11 inherit edges
sentrux gate — structural regression check

Quality:      4693 -> 4700
Coupling:     0.79 → 0.79
Cycles:       3 → 3
God files:    3 → 3

Distance from Main Sequence: 0.33

✗ DEGRADED
  ✗ Complex functions increased: 56 → 65

[codecov]

Codecov Report

❌ Patch coverage is 78.48780% with 441 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.63%. Comparing base (8d94e67) to head (86b5a17).

Files with missing lines	Patch %	Lines
factory/outer_loop/direct_evaluator.py	21.36%	167 Missing and 6 partials ⚠️
factory/cli/outer_loop.py	11.30%	102 Missing ⚠️
factory/outer_loop/engine.py	84.89%	23 Missing and 22 partials ⚠️
factory/outer_loop/mutations.py	88.63%	21 Missing and 24 partials ⚠️
factory/outer_loop/filesystem.py	79.79%	14 Missing and 6 partials ⚠️
factory/outer_loop/designer.py	85.85%	4 Missing and 10 partials ⚠️
factory/outer_loop/subset.py	86.90%	8 Missing and 3 partials ⚠️
factory/workflow/primitives.py	73.52%	4 Missing and 5 partials ⚠️
factory/outer_loop/run_evolution.py	88.13%	5 Missing and 2 partials ⚠️
factory/outer_loop/harbor_evaluator.py	94.28%	3 Missing and 1 partial ⚠️
... and 5 more

❌ Your patch check has failed because the patch coverage (78.48%) is below the target coverage (79.00%). You can increase the patch coverage or adjust the target coverage.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1275      +/-   ##
==========================================
- Coverage   86.26%   85.63%   -0.63%     
==========================================
  Files         211      229      +18     
  Lines       23123    25173    +2050     
  Branches     3656     3980     +324     
==========================================
+ Hits        19946    21557    +1611     
- Misses       2331     2687     +356     
- Partials      846      929      +83     

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