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Unify output directory structure with out_app_flag=2 - #8159

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mohanchen wants to merge 12 commits into

deepmodeling:developfrom

mohanchen:2026-10-16-b

Open

Unify output directory structure with out_app_flag=2#8159
mohanchen wants to merge 12 commits into
deepmodeling:developfrom
mohanchen:2026-10-16-b

Commits on Oct 16, 2026
- refactor(out_app_flag): change out_app_flag from bool to int and add unified output directories
  abacus_fixer
  committed
  ae461dd
- feat(output): use unified subdirectories when out_app_flag=2
  abacus_fixer
  committed
  2545b1b
- test(io): update directory expectations for out_app_flag default
  abacus_fixer
  committed
  1beabad
- refactor(io): migrate remaining out_app_flag bool usage to int
  abacus_fixer
  committed
  a4ce9a3
- chore: remove accidentally committed quality report file
  abacus_fixer
  committed
  5adf04b
- fix(io): use local cached directory variables in ctrl_output_fp
  abacus_fixer
  committed
  e734403
- test(integrate): fix WFC file path in props_cube.sh for out_app_flag=0
  abacus_fixer
  committed
  9254e95
- feat(io): create subdirs on demand and route dmk/lx/rr/tr to MAT
  abacus_fixer
  committed
  00ece15
Commits on Oct 18, 2026
- feat(io): route dmr/tr/rr/dh/ds/lx outputs to MAT directory
  
  abacus_fixer
  and
  claude
  committed
  a77e356
- feat(io): unify STRU output directory and naming for relax and MD
  
  abacus_fixer
  and
  claude
  committed
  3a38485
- feat(md): replace md_restartfreq with out_freq_ion + out_stru
  
  abacus_fixer
  and
  claude
  committed
  aabef5f
- fix(md): start MD STRU numbering from 1 (like relax)
  
  abacus_fixer
  and
  claude
  committed
  443c337