Foundry repo
Local clone: /Users/jxc755/projects/repositories/foundry
GitHub: https://github.com/jmchilton/foundry
Design docs (in repo): docs/ARCHITECTURE.md, docs/HARNESS_PIPELINES.md, docs/MOLDS.md, docs/COMPILATION_PIPELINE.md, docs/CORPUS_INGESTION.md, docs/GXY_SKETCHES_ALIGNMENT.md, docs/COMPONENT_ARCHON.md.
Glossary (terminology, agent-loaded): content/glossary.md.
Originals before move (preserved): vault/projects/workflow_state/old/.
Adjacent projects
gxy-sketches — corpus of routing/decision-aid sketches distilled from nf-core + IWC; consumed by gxy3 (chat-driven app). Owned by another contributor; field-name parity is the only entanglement. See docs/GXY_SKETCHES_ALIGNMENT.md in foundry.
/Users/jxc755/projects/repositories/gxy-sketches
Galaxy-brain-local notes (not Foundry)
Galaxy-brain influence reference (kept here, not in Foundry): /Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/skills/COMPONENT_GALAXY_BRAIN.md
Galaxy / Nextflow workflow-testing background research (Foundry-relevant; pending conversion to research/component notes):
/Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/skills/COMPONENT_GALAXY_WORKFLOW_TESTING.md
/Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/skills/COMPONENT_NEXTFLOW_WORKFLOW_TESTING.md
Prior art (reference, not carried forward):
- /Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/skills/SKILLS_NF.md
- /Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/skills/SKILLS_REPORTS.md
Corpus
IWC workflow fixtures (cleaned gxformat2 versions):
/Users/jxc755/projects/repositories/workflow-fixtures
(consume iwc-format2/ subdirectory)
Tooling worktrees
Skill Development Worktree: /Users/jxc755/projects/worktrees/galaxy-skills/branch/wf_dev
Galaxy / Python version of gxwf R&D Branch: /Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state
gxformat2 R&D Branch: /Users/jxc755/projects/worktrees/gxformat2/branch/abstraction_applications
TypeScript gxwf R&D Branch: /Users/jxc755/projects/worktrees/galaxy-tool-util/branch/skills
Existing skills (prior art being replaced)
find-shed-tool skill design — feeds the discover-shed-tool Mold; the hand-authored skill form does not carry over:
/Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/old/PLAN_SEARCH_CLI.md
gxwf-cli skill (help-text dump) — to be replaced by the gxwf-cli Mold + content/cli/gxwf/ manual pages:
~/.claude/skills/gxwf-cli
Research notes
User Defined Tools (PR 19434): /Users/jxc755/projects/repositories/galaxy-brain/vault/research/PR 19434 - User Defined Tools.md
gxformat2 parsing & syntax: /Users/jxc755/projects/repositories/galaxy-brain/vault/research/Component - gxformat2 Parsing and Syntax.md
Collection Tool Execution Semantics: /Users/jxc755/projects/repositories/galaxy-brain/vault/research/Component - Collection Tool Execution Semantics.md