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feat(integrations): sync upstream plugin compatibility updates - #4
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Port shared upstream platform fixes from compound-engineering v3.9.3 while preserving ce-datascience's health data science scope. Add CODEX_HOME-aware installs, Codex root/hook handling, current source-agent filenames, curated workflow skill updates, and public release/bug-report support skills. Verified with targeted smoke installs, release validation, diff checks, and the full Bun test suite.
Add Codex hook bundle typing and standalone converter wiring, rebuild managed hook ownership indices after each merge, and back up malformed hooks.json before replacement. Verified with bunx tsc --noEmit, focused Codex tests, release validation, diff check, and the full Bun test suite.
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sajor2000
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Oct 21, 2026
Close the journal-selection half of audit gap #5 with a new skill that matches a finished manuscript or abstract to candidate journals: - builds a 5-8 candidate pool from each journal's own aims-and-scope page read via web tools, never from memory or a third-party summary; - gathers scope-fit evidence by searching PubMed restricted to each candidate journal for similar recent studies (count and recency); - runs a legitimacy screen verifying each candidate's indexing claims against the NLM Catalog or DOAJ, flagging unverifiable claims, copycat names, and APC-only venues instead of silently dropping or accepting them; - applies the author's must-haves (indexing, access policy and fees, review speed) as hard filters, ranks with every cell sourced or marked unknown, and recommends a target plus two backups, leaving the choice to the author. Sourcing rules are the core discipline: no impact factor, acceptance rate, turnaround, or APC from memory; every metric carries a source URL and date or is marked unknown. Egress mirrors the other research skills: searches carry study topics, designs, and journal names only. The listing budget rises from 11,500 to 11,700 for the 68th skill (11,686 total, the same ~172-char average per skill), and every displayed count surface (READMEs, website, brand SVG) moves 67 -> 68. Eval sets follow the skill-creator contract (3 evals, 10/10 triggers). The audit doc records gap closures: #2 (PR #138), #4 (PR #140), and the journal-selection half of #5, with the ICMJE COI half left open as a decision. Description fingerprints regenerated from history.
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Summary
This sync brings the fork up to the useful shared compatibility layer from upstream
compound-engineering-v3.9.3without turningce-datascienceback into a generic software-engineering plugin. Codex profile installs now respectCODEX_HOME, Codex writer output can target an actual Codex root, managed Codex hooks are preserved and replaced safely, and source agents use the current.mdconvention while legacy.agent.mdparsing remains covered.The workflow surface is also more professional for public users: plan and brainstorm can render markdown or HTML while preserving SAP and health research behavior, PR feedback resolution keeps statistical methodology concerns first-class, session discovery covers Claude/Codex/Cursor more robustly, and release-notes plus bug-report skills are available as support workflows. Software/product-only upstream skills were intentionally not imported.
Verification
CODEX_HOMEbun run release:validategit diff --checkandgit diff --cached --checkbun test