chore: keep agent working notes local; gitleaks allowlist no longer needs the scrubbed key value

Merge branch 'lane/heuristic-lumiere-cee83f'

docs: Loveless prod e2e verified (both sc UMAPs) + Werba pseudobulk→DESeq2 clean; ADR-0006 items 7/8 closed

fix: dataset_load Path P now returns the h5ad; re-pin biodata-registry 0.1.16

Merge fix/lfs-prepush-chain: git-lfs pre-push chained into the security hook

fix(hooks): chain git-lfs pre-push after the ADR-0014 security scan

Merge feat/what-happened-panel: run-provenance panel (tools + datasets per step)

feat(ui): collapsed 'what happened' provenance panel after every run

Merge fix/surface-csv-schema: CSV schema in DE return + no schema-sniff re-reads

feat(de): surface the results-CSV schema; prompt bans schema-sniff re-reads

Merge feat/dataset-load-executor: one-call registry-aware dataset loading

feat(datasets): dataset_load — execute the loading plan by dataset_id in one call

Merge feat/nested-batch-advisor: nested-batch refusal recommends per-level contrasts

feat(de): nested-batch guard now recommends the de-confounded alternative

Merge feat/de-low-count-filter: default low-count filter + stat-ranking rule

feat(de): default low-count gene filter pre-DESeq2 + stat-ranking prompt rule

Merge fix/export-scope-current-question: exports scoped to the current question

fix(ui): scope exports to the current question's run, not the whole session

Merge fix/raise-agent-timeout: raise agent timeout to 2700s

fix(ui): raise agent timeout 1200s -> 2700s for long-running analyses

Merge feat/upload-assembly-tsvs: assemble raw TSVs inside the upload gate

feat(upload): assemble raw counts/TPM/metadata into an h5ad inside the gate

Merge fix/pdf-figure-placement: PDF figures were drawn off-page

fix(export): figures were drawn off the right edge of every PDF

Merge feat/mouse-prompts-note: mouse ad-hoc guidance in prompts.yaml

feat(prompts): mouse ad-hoc data guidance (Gap 3 of the mouse-support scope)

Merge fix/de-libsize-preflight: library-size QC pre-flight in the DE tool

feat(de): sample-level library-size pre-flight in decoupler_differential_expression

feat(mouse-intake): read Carl's real Novogene metadata Excel directly

Merge fix/enrichment-nonfinite: drop NaN/inf DE stat genes before ulm

fix(enrichment): drop non-finite DE stat genes before ulm; report n_dropped_nonfinite

Merge fix/deseq2-subset-query: apply subset_query on the DESeq2 branch

fix(de): apply subset_query on the DESeq2 branch too

Merge feat/mouse-intake: mouse staging script + nested-batch guard

feat(mouse): thin mouse-intake path — staging script, ENSMUSG→MGI map, nested-batch guard

chore(security): refresh SBOM for the biodata-registry 0.1.14 → 0.1.15 pin

fix(tools): select the contrast row positionally so top_table cannot fail the tool

fix(tools): keep top_table inside the executor's 4000-char output cap

merge: dev's n_post_analysis_reads instrumentation into the top_table fix

perf(tools): return the reporting table inline from every chain-terminating tool

Revert "perf(agent): pin results artifacts across the memory window"

merge: instrument n_post_analysis_reads (the 808b91d re-read claim)

feat(metrics): instrument n_post_analysis_reads to test the 808b91d claim

perf(agent): pin results artifacts across the memory window

merge: rename the limma probe out of pytest's collection path

chore(scripts): rename the limma probe so pytest stops collecting it

merge: bare pytest works; pre-commit abort documented

chore(tests): make a bare `pytest` work, and document the pre-commit abort

merge: inline top table closes the reporting tail

fix(reporting): return the top table inline so the report needs no re-read