Move generic optimization behavior to runtime owners (#323)

[trissim]

Store mutations now invalidate their owned query caches, and shared optimization mechanics derive from core owners. Provider-independent object columns, persistent kernel preparation, bounded cache storage/lifetime and the logger-bound profiler move to their shared layer. Numerical keys, algorithms, provider effects and the separate CP module-context profiler retain their domain owners. Obsolete globals, classes and forwarding paths are removed.

The warmed-parent review issue is fixed in ProcessLocalBoundedCache's cooperative subclass hook: each declared subclass owns its singleton and construction lock. Controls cover parent-before-child for plain/registered/identity-bound families, eight-way concurrent child creation, slotted dataclass children, warmed synchronized diamond inheritance, MRO/hook cooperation, LRU eviction and registered cleanup. Four inheritance controls fail before the fix and pass afterward. No consumer workaround or mirror registry is added.

Two source-projection tests also leaked their global microscope configuration into later checkpoint tests. The existing ObjectState GlobalContextValues capture/apply owner now scopes those edits, preserving saved/live projections and absent contexts. Unchanged main passes the checkpoint module alone but fails 2/101 in the specified module order; the corrected broad sequence passes with strict original address/pixel/calibration assertions. This fixes #336 without changing microscope admission or fabricating HTD metadata.

Latest production f7b39a2a4 includes main f24a828da and exact dependency pins, including PolyStore 84f322e. The final documentation commit has an identical production/dependency/benchmark/script/test tree. 1,538 local tests and 42 subtests pass, with one existing optional Napari skip and two unchanged watershed warnings. Original CI-pinned R0 and original NRA R1 pass without increases; complete ClassDef census retains 5,129 declarations, 5,117 projected and all 12 OPEN. Repeated complete native-reference qualification passes 30/30, every difference_count=0, on this latest production source. Existing 1e-6 numerical tolerances and exact discrete/identity/declared-image checks remain.

Matched ordinary ABBA timings identify prior synced production 68aed451f / main 8c512d404; they are not relabeled as newer-source timings. ImagingFlow mean execution is 14.482s main / 14.573s branch and total 16.682s / 17.126s, including a 0.354s compilation increase. Advanced segmentation execution is 9.442s / 8.999s and total 12.386s / 12.101s. These small samples do not establish neutrality or a general speedup. The residual ImagingFlow total difference is retained for performance work under #162; the latency target is not claimed complete.

Current validation, ownership and reproduction and its authenticated evidence archive contain exact recipes, source/pins, main and warmed-parent negative controls, local XML, original guards/census, final native observations/generated pipeline sources/measured receipts and all ordinary timing samples. Prior guarded NRA movements are separate from authored semantic behavior. Removed private import paths remain an explicit external dynamic boundary.

Ready-server startup/shutdown are excluded from pipeline clocks. Mandatory registry/kernel preparation precedes clocks, and tests/audits/builds/replays do not overlap timed pipelines. Native scientific outputs are retained references; old native clocks are not fresh speedup evidence. Native/scaling figures and performance grinding continue under #162.

Fixes #323. Fixes #336.

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[trissim]

Concrete inheritance/new-case failure in the touched shared lifetime owner; please pick this up in the existing PR rather than a competing patch. On exact main b31807d and PR head 3417e36: define ParentCache(ProcessLocalBoundedCache), obtain ParentCache.process_cache(), store a parent-only value, then define ChildCache(ParentCache) and obtain ChildCache.process_cache(). Both revisions return the same ParentCache instance (actual type ParentCache), and ChildCache sees the parent-domain value. This violates the declared one-singleton-per-concrete-subclass contract; it predates this PR, so I am not calling it an introduced regression. The new lock does not fix inherited _process_cache identity. Current tests cover sibling isolation/one-leaf concurrent construction but not warmed-parent extension. Please fix declaration identity in the shared lifetime owner, preserve cooperative MI/MRO, concurrency, bounded values and registry cleanup, with parent-before-child and diamond behavior controls; no consumer workaround or new mirror registry. Original read-only exact-source reproducer failed as expected in 83ms/9.9M, retained at /home/ts/wt/openhcs-issue-batch-20260929/runtime-cache-review-20261001/reproduce_subclass_identity.py and original-reproduction.log. Existing PR326/issue323 owner keeps source ownership; parent is tracking review closure. No native/science/runtime slot or installed environment changed.