## genomoncology/biomcp — v0.8.19…v0.8.20

_78 commits._

### Features
- **Add disease key feature summaries** (36e6f92)
- **Add code log for disease definition change** (3f8378f)
- **Add code log for target family change** (c647d78)
- **Add code-review repair tests for atc-exact and mechanism_of_action alignment** (fe1e095)
- **Add March code log for purine mechanism audit** (46d3261)
- **Apply code-review repairs: extend gitignore coverage assertion, add bare-python and targeted-heading tests** (77e95e5)
- **Add BioMCP quality ratchet checks** (4ca4a49)
- **Merge Add cross-entity See-also links: drug→pgx, gene→pgx, disease→study, zero-result→discover** (0b14216)
- **Add cross-entity see-also links** (1a83489)
- **Add ticket code log** (be19df6)
- **Add study top-mutated and disease literature fallback** (7e2f2a5)
- **Add repo-contract tests and link examples/README.md index entries** (c2a6b43)
- **Merge Architecture docs — add chart architecture section and update version string** (4bd1315)
- **Architecture docs — add chart architecture section and update version string** (d827d7e)

### Fixes
- **fix: repair three pre-existing contract test failures** (241d81f)
- **Merge Fix remaining BioASQ product gaps: protein truncation, variant targets, disease features** (7af8774)
- **Fix BioASQ protein truncation and variant targets** (f2bb228)
- **Fix isoform template blank line between Isoforms and Function** (f75f822)
- **Add code-review repair tests and fix isoform template whitespace** (81c5efb)
- **Merge Fix gene-to-pgx and disease-to-drug See-also commands** (27fedd2)
- **Fix gene and disease see-also pivots** (ecc6a43)
- **Allow study top-mutated through MCP allowlist; fix list_reference summary** (0a092cd)
- **Fix large PMC OA fulltext downloads** (18fd7e4)
- **Merge Bug fix — harden GWAS variant section for live decode failures** (cccc344)
- **Bug fix — harden GWAS variant section for live decode failures** (4f1155e)
- **Merge Bug fix — batch --json add _meta contract** (54639fe)
- **Bug fix — batch --json add _meta contract** (e985b27)
- **Merge Security fix — MCP allowlist permits mutating study download command** (8c0d79a)
- **Security fix — MCP allowlist permits mutating study download command** (fe37826)
- **Merge Security fix — remove partial API key from health output** (16dd133)
- **Security fix — remove partial API key from health output** (20a4cb1)
- **Merge Documentation consistency audit — 40-item copywriting fix pass** (041cb62)
- **Documentation consistency audit — 40-item copywriting fix pass** (b2e0c11)

### Backend
- **Merge v0.8.20 release — changelog, mustmatch shim removal, tag** (77f3142)
- **Apply code-review fixes: BIOMCP_BIN, default rindopepimut spec, source-licensing CIViC update** (7d9b990)
- **Merge Disease phenotypes: distinguish defining features from comprehensive HPO list** (73552ae)
- **Disease phenotypes: distinguish defining features from comprehensive HPO list** (8aaa908)
- **Apply code-review fixes: colon-after-cue extraction, frequency-rank test, degradation test** (7f585df)
- **Merge Stop truncating disease definitions — show full characterization text** (cbdb0af)
- **Show full disease definitions** (b696352)
- **Merge Show protein legacy names alongside gene symbols** (47aa494)
- **Update docs for legacy protein name feature** (7242393)
- **Show legacy protein names in gene protein output** (a88471f)
- **Merge Show drug target family name alongside individual targets** (710e257)
- **Apply code-review repairs: UTF-8-safe prefix, missing edge-case tests, spec negatives** (4f1a08f)
- **Show drug target family alongside targets** (7c6d479)
- **Merge Surface UniProt protein isoforms in gene protein section** (a6e4fb7)
- **Surface UniProt isoforms in gene protein section** (93c6849)
- **Merge Audit drug mechanism labels for purine analog completeness** (dfbda74)
- **Improve purine drug mechanism search coverage** (2d4d307)
- **Merge Show variant legacy nomenclature alongside HGVS** (7f404c3)
- **Apply code-review repairs: representative alias tests, path normalization, schema doc** (51ee24b)
- **Show legacy variant names alongside HGVS** (e4abb97)
- **Merge Architecture docs: See-also contract, discover grammar, CI description, post-tag proof** (1b5b07b)
- **Remove .march/code-log.md from git tracking (violates repo-cleanup contract)** (8bb4a0d)
- **Apply code-review repairs: dynamic version tag helper, relax discover spec assertion** (d2c550e)
- **Document discover and see-also architecture contract** (b5f29a8)
- **Merge Repo cleanup: remove tracked .march artifacts, restore test-contracts** (874fe02)
- **Restore repo cleanup contract** (3e16a6c)
- **Merge Wire quality ratchet into BioMCP make check** (1883a35)
- **Apply code-review repairs: lint regex and expanded contract tests** (3593591)
- **Improve spec/21 H1 intro prose to 3 sentences** (d2dd192)
- **Apply code-review repairs: missing tests and spec assertions** (199cf27)
- **Merge Close 4 BioASQ product gaps: fulltext size, rare disease phenotypes, somatic mutations, rare drug indications** (1287a57)
- **Remove .march/code-log.md from git tracking** (f081739)
- **Merge Repo cleanup — gitignore, rename, consolidate** (0f62d65)
- **Clean up repo layout and example paths** (30c78c6)
- **Merge Help architecture overhaul: self-teaching CLI for agent navigation** (779ec63)
- **Help architecture overhaul: self-teaching CLI for agent navigation** (aaedb28)
- **Implement help architecture routing updates** (66988be)
- **Update docs and MCP contracts for worked examples** (07370bc)
- **Rewrite CLI help surfaces and skill catalog** (3bbd5b7)
- **Remove broken skill symlinks (create-ticket, plan, plan-frontier)** (fb58fb1)
- **Merge UX polish — --since alias visibility, discover duplicate next_commands, chart help, phase canonical** (257f7a8)
- **UX polish — --since alias visibility, discover duplicate next_commands, chart help, phase canonical** (2222b5f)

### Tests
- **test: apply code-review tightening for v0.8.20 contracts** (3012d68)
- **test: prove v0.8.20 release prep** (7043a52)

### Chore
- **build: prepare v0.8.20 release** (e8dcc55)

_Recap by [Repo Wrapped](https://repowrapped.com/gh/genomoncology/biomcp?utm_source=github-action)._