fix: carry plugin-created .factory/ subdirs into worktrees

[shivchander]

Closes #1263

Changes

• After the existing symlink/copy logic and per-cycle fresh directory creation in create_worktree, iterate over any remaining subdirectories in the source .factory/ and copy them to the worktree
• Skips entries already present (symlinked shared entries, copied entries, or freshly-created per-cycle dirs like strategy/reviews/state) via a dst.exists() check
• Only copies subdirectories, not loose files — plugin intake dirs like .factory/buildroot/ are the target

[github-actions]

Sentrux Quality Report

Absolute

Scanning ....
[scan] git ls-files: 609 total, 597 kept, 12 dropped (ext:12, meta:0, big:0)
[build_project_map] 597 files, 102 unique dirs, 94 cache misses, 2.5ms
[resolve] 1088 resolved, 1537 unresolved (of 2625 total specs)
[resolve_imports] project_map 2.6ms, suffix_idx 1.1ms, suffix_resolve 15.3ms, total 19.1ms
[build_graphs] 597 files | maps 1.5ms, imports 19.2ms, calls+inherit 4.9ms, total 25.6ms | 1087 import, 8621 call, 11 inherit edges
sentrux check — 3 rules checked

Quality: 4789

✗ [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: 609 total, 597 kept, 12 dropped (ext:12, meta:0, big:0)
[build_project_map] 597 files, 102 unique dirs, 94 cache misses, 2.6ms
[resolve] 1088 resolved, 1537 unresolved (of 2625 total specs)
[resolve_imports] project_map 2.7ms, suffix_idx 1.0ms, suffix_resolve 15.3ms, total 19.0ms
[build_graphs] 597 files | maps 1.5ms, imports 19.1ms, calls+inherit 5.0ms, total 25.7ms | 1087 import, 8621 call, 11 inherit edges
sentrux gate — structural regression check

Quality:      4790 -> 4789
Coupling:     0.79 → 0.79
Cycles:       3 → 3
God files:    3 → 3

Distance from Main Sequence: 0.38

✗ DEGRADED
  ✗ Complex functions increased: 53 → 54

[codecov]

Codecov Report

❌ Patch coverage is 66.66667% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.33%. Comparing base (4129ba2) to head (fb516de).

Files with missing lines	Patch %	Lines
factory/worktree.py	62.50%	1 Missing and 2 partials ⚠️

❌ Your patch check has failed because the patch coverage (66.66%) 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    #1265      +/-   ##
==========================================
- Coverage   86.34%   86.33%   -0.01%     
==========================================
  Files         211      211              
  Lines       23054    23062       +8     
  Branches     3627     3631       +4     
==========================================
+ Hits        19906    19911       +5     
- Misses       2308     2309       +1     
- Partials      840      842       +2     

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