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making rec_backend=pcg and rec_backend=gridding comparable for side-by-side testing in abinitio3D
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doc/implementation_notes/Local-linear_diffusion-map_pre-image.md renamed to doc/implementation_notes/completed/Local-linear_diffusion-map_pre-image.md

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doc/implementation_notes/continuous_inplane_rotation_polar.md renamed to doc/implementation_notes/completed/continuous_inplane_rotation_polar.md

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doc/implementation_notes/diffusion_maps_manifoldem_review.md renamed to doc/implementation_notes/completed/diffusion_maps_manifoldem_review.md

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doc/implementation_notes/qsys_scheduler_completion_bug_report.md renamed to doc/implementation_notes/completed/qsys_scheduler_completion_bug_report.md

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doc/implementation_notes/pcg_nonuniform_code_review.md

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doc/implementation_notes/pcg_priors.md

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@@ -3735,6 +3735,24 @@ and gridding `_pproc` maps are no longer masked a second time. The sidecar
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moved to `simple_halfmap_diagnostics` (`write/read_support_provenance`,
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file name unchanged). Uncompiled; user compiles and runs the comparison.
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### Record (2026-09-09c): backend comparison review -- shared observation, transactional sidecar, hard domain + window, cost records
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Findings of `doc/refactoring_notes/abinitio3d_reconstruction_backend_comparison_review.md`
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verified against the code and acted on:
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| finding | verified | change |
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|---|---|---|
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| 3.1 cropped observations prepared differently | yes: gridding norm -> Fourier crop -> taper at crop box (`prep_imgs4rec`), PCG norm -> taper at native box -> native plane of the crop disk (three accumulation sites); no-crop order also differed (taper/norm) | `prep_rec_observation` in `simple_matcher_ptcl_io`, called by `prep_imgs4rec` (crop step) and all three PCG accumulation loops; `test=pcg_recon` stage 13 parity gate |
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| 3.2 sidecar lifecycle | yes: stage-boundary `simple_rename` of the state volume left `<vol>_pcg_support.txt` behind (base warm start refused at the next stage's first iteration), final/symmetric copies unpaired, sidecar written before the map | `copy/rename/remove_support_provenance` in `simple_halfmap_diagnostics`, applied at the abinitio3D stage rename, final and symmetric copies, refine3D start-volume rename, noise starts and imports; PCG masters write the map before the sidecar |
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| 4.1 wall time only | yes | per-part bench files with context and thread-seconds; master phase line with threads, thread-seconds and peak RSS |
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| 4.2 support formulations not equal | yes: where `0 < P < 1` the converged constrained solution is the unconstrained one (`P` cancels), so the band depended on the CG state | hard solve domain `window > 0` + one soft output window (`install_support`, `window_mul`, `window_div`; `PCG_HARD_SOLVE_SUPPORT` toggle); stage 14 regressions |
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The window band regression (stage 14a) asserts, over shells with window in
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[0.15, 0.85], that the constrained 40-iteration solve equals the windowed
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unconstrained solve within 15% RMS; 14b that six repeated two-iteration
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output-space warm starts keep the band RMS within 10%. Uncompiled; the user
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compiles, runs the test gate and the paired comparison.
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## 11. The NU machinery as the prior infrastructure
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The nonuniform-regularization machinery

doc/implementation_notes/pfcrt_audit_a6ae317ae_vs_head.md

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