M3 — donor non-PLS source move: STATUS¶

Date: 2026-05-21 (same merge sprint) Branch: merge/import-donor Pushed: pending commit (this report ships with it)

What was done¶

222 donor source files were git mv-moved from _donor/nirs4all-methods/cpp/src/core/{preprocessing,augmentations,splitters,filters,utilities}/ to their final positions under cpp/src/core/<category>/. Blame chain preserved via git mv for every file (status R in git status).

Category move	Files	From	To	Note
Preprocessing	94	`_donor/.../cpp/src/core/preprocessing/{11 subcats}/`	`cpp/src/core/preprocessing/{11 subcats}/`	per-subcategory move (baselines, derivatives, feature_selection, orthogonalization, resampling, scaling, scatter, signal_conversion, smoothing, specialized, wavelets)
Augmentation	82	`_donor/.../cpp/src/core/augmentations/{10 subcats + 2 root files}/`	`cpp/src/core/augmentation/{10 subcats}/` + 2 root files	plural → singular rename per §11/M3 decision (drift, edge_artifacts, environmental, mixup, noise, random, scattering, spectral, splines, wavelength)
Splitters	20	`_donor/.../cpp/src/core/splitters/`	`cpp/src/core/splitters/`	flat
Filters	16	`_donor/.../cpp/src/core/filters/`	`cpp/src/core/filters/`	includes `_vendored/` subdir
Utilities	10	`_donor/.../cpp/src/core/utilities/`	`cpp/src/core/utilities/`	flat
Total	222

Common-core duplicates deleted (M3.2)¶

Files that had landed at cpp/src/core/common/ during M2.5 were removed from their donor location:

_donor/nirs4all-methods/cpp/src/core/context.cpp           (deleted)
_donor/nirs4all-methods/cpp/src/core/context.hpp           (deleted)
_donor/nirs4all-methods/cpp/src/core/status.cpp            (deleted)
_donor/nirs4all-methods/cpp/src/core/status.hpp            (deleted)
_donor/nirs4all-methods/cpp/src/core/matrix_view.cpp       (deleted)
_donor/nirs4all-methods/cpp/src/core/matrix_view.hpp       (deleted)
_donor/nirs4all-methods/cpp/src/core/version.cpp           (deleted)
_donor/nirs4all-methods/cpp/src/core/version.hpp           (deleted)
_donor/nirs4all-methods/cpp/src/core/parallel.hpp          (deleted)
_donor/nirs4all-methods/cpp/src/core/linalg.hpp            (deleted)
_donor/nirs4all-methods/cpp/src/core/common/               (entire subtree deleted — landed at cpp/src/core/common/ in M2.5)

After M3, _donor/nirs4all-methods/cpp/src/core/ is empty (verified by find ... -type f returning 0).

Stale-reference cleanup (M3.3)¶

File	Reference	Action
`_donor/.../parity/python_generator/src/n4m_parity_aug_spectral_ref/__init__.py`	`cpp/src/core/augmentations/{wavelength, spectral}/` (comment)	Updated to `cpp/src/core/augmentation/...` (singular)
`_donor/.../bindings/r/n4m/src/libn4m/src/c_api/c_api_preprocessing.cpp`	`cpp/src/core/preprocessing/...` (comment)	Already correct — no change
`_donor/.../bindings/r/n4m/src/libn4m/src/c_api/c_api_resampling.cpp`	`cpp/src/core/preprocessing/resampling/` (comment)	Already correct — no change
`_donor/.../cpp/src/CMakeLists.txt`	89 `core/augmentations/...` and `core/preprocessing/...` source entries	Marked BROKEN with a header note; not rewritten (this CMakeLists is dormant — pls4all does not activate it, and the unified CMakeLists lands in M5/M6)

Build verification (M3.4)¶

pls4all build and tests remain green after the M3 moves, because the M3 moves are purely additive from pls4all’s build-system perspective:

pls4all’s cpp/src/CMakeLists.txt enumerates explicit source files under cpp/src/core/<file>.cpp (no file(GLOB ...) patterns), and the source list is unchanged.
The moved donor sources now live at cpp/src/core/<category>/<sub>/<file>.{c,h}, paths that pls4all’s CMakeLists does not reference.
The deleted _donor/.../cpp/src/core/{context,status,matrix_view,version,parallel,linalg.hpp,common/} copies were not consumed by anything in pls4all’s build either.

$ cmake --build --preset dev-release
ninja: no work to do.
$ ./build/dev-release/cpp/tests/n4m_tests
=== 265 run, 0 failures, 0 skipped ===

Roadmap gate evaluation¶

The roadmap M3 gate (MERGE_ROADMAP.md §9 row M3):

donor fixtures still pass against the moved sources; git blame -C -C -C chains back to donor commits

Sub-gate	Status	Notes
`git mv` preserves blame chain	✅ verified	All 222 moves are `R` status (rename) in `git status`. `git blame -C -C -C cpp/src/core/preprocessing/baselines/airpls.c` reaches donor’s original commits.
Donor fixtures pass against moved sources	⚠️ deferred	The donor’s C++ test binary (`n4m_tests` at `_donor/.../cpp/tests/`) is not wired into pls4all’s build yet. The unified test runner lands in M5/M6. The Python parity generator (the M2.5-aware part) sees no path drift because Python imports work by symbol, not by C source path.
pls4all-fixture C++ tests still pass	✅ 265/265	unchanged by M3

File-count budget after M3¶

cpp/src/core/
├── common/                    31 files       (landed in M2.5)
├── preprocessing/{11 subs}/   94 files       ← NEW from donor in M3
├── augmentation/{10 subs}/    82 files       ← NEW from donor in M3
├── splitters/                 20 files       ← NEW from donor in M3
├── filters/                   16 files       ← NEW from donor in M3 (incl. _vendored)
├── utilities/                 10 files       ← NEW from donor in M3
├── <models/, selection/, diagnostics/, aom_pop/, transfer/, pipeline/>     placeholders only (target for M4 split of pls4all's model.cpp + extra_pls.cpp)
└── <pls4all flat sources at this level>      58 files (unchanged in M3 — M4 splits them)

Total under cpp/src/core/: ~311 files post-M3 (was ~89 after M2).

What is NOT done in M3¶

Per roadmap §9, the following stay open and land later:

M4 — pls4all source split: 6188 lines across model.cpp (4541 L) + extra_pls.cpp (1647 L) split into ~28 target files. Detailed plan at docs/merge/M4/SPLIT_PLAN.md (produced by an Explore agent in parallel with M3).
M5 — ABI rename: n4m_* → n4m_* mechanical pass. Until then, pls4all’s flat sources still use n4m_* symbols.
M6 — unified C ABI headers: split umbrella header into per-category headers.
M7 — unified parity gate: wires both halves into one runner.
The donor’s broken _donor/.../cpp/src/CMakeLists.txt is marked broken but kept for archeology; deletion happens in M6 when the unified build wiring lands.

Risk register update¶

Risk	Status
Move breaks pls4all build	✅ Confirmed safe (additive only — pls4all CMakeLists references unchanged)
Move breaks donor’s standalone build	Accepted — donor build was already dormant in pls4all repo; flagged in CMakeLists header
Blame loss on rename	Mitigated — `git mv` used throughout; status shows R (rename), not D+A
Plural-singular rename causes downstream confusion	Mitigated — singular `augmentation` adopted everywhere; only stale reference (the Python parity doc-string) updated

Next: M4 — pls4all source split¶

Plan ready at docs/merge/M4/SPLIT_PLAN.md. 7-phase extraction (~34 commits), starting with helper-extraction → core PLS → derived → classification → sparse → specialized/ensembles/transfer → core dispatch.