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"

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

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

fix(scoring): close the six PROGENy per-sample gaps from the GSE205154 eval

feat(auth): OAuth + allow-list gate on the specialist UI (ADR-0012) (#1)

refactor: move writable-dir constants to core.paths, fix workflow->tools layer violation

style: apply ruff lint --fix + ruff format across the tree

Merge remote-tracking branch 'origin/main' into feat/sandbox-executor

feat(integrity): ADR-0010 on-load verify for GEO series-matrix loads

feat(auth): ADR-0012 identity seam + identity into audit trace (Now slice)

feat(logging): ADR-0013 audit-trace redaction (secret/credential/PII scrubbing)

feat(integrity): wire ADR-0010 on-load verify + re-pin 0.1.9 (deploy slice)

refactor(integrity): unify ADR-0010/0011 into one src/core/integrity.py

feat(uploads): ADR-0011 manual-upload safety gate ("Now" slice)

feat(loveless): Role-2 signature consumable — resolve private signature URLs

perf(mcp): wire persistent HTTP MCP server + in-memory adata cache + step timing

refactor(loader): centralize authenticated URL->local resolution

ADR-0001 Phase 1, step 4: meta-analysis engine (Mode B late integration)

ADR-0001 Phase 0: cross-dataset integration contract + specs

Make decoupleR method-limitations text deterministic

Cap conversation history and code-output size to bound credit cost

Align project layout with HF Spaces and FastMCP conventions