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Add FermiLink skills for hail
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‎skills/.compile_report.json‎

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{
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"compile_memory_path": "skills/.evidence/memory.md",
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"compiled_package_id": "hail",
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"evidence": {
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"core_skills": [
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"hail-api-and-scripting",
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"hail-test",
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"hail-build-and-install",
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"hail-getting-started",
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"hail-dev-docs",
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"hail-troubleshooting"
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],
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"evidence_dir": "skills/.evidence",
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"files": [
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"skills/.evidence/hail-api-and-scripting.md",
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"skills/.evidence/hail-test.md",
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"skills/.evidence/hail-build-and-install.md",
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"skills/.evidence/hail-getting-started.md",
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"skills/.evidence/hail-dev-docs.md",
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"skills/.evidence/hail-troubleshooting.md"
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]
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},
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"generation": {
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"docs_only": false,
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"generator_script": "sci-skills-generator/scripts/generate_skills_folder.py",
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"max_skills": 30,
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"return_code": 0,
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"status": "ok"
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},
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"mode": "compile",
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"pass_scope_diffs": {
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"pass_2": {
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"added": [
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"skills/hail-advanced-topics/SKILL.md",
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"skills/hail-advanced-topics/references/source_map.md"
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],
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"changed": [
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"skills/hail-advanced-topics/references/source_map.md",
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"skills/hail-api-and-scripting/SKILL.md",
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"skills/hail-build-and-install/SKILL.md",
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"skills/hail-dev-docs/SKILL.md",
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"skills/hail-getting-started/SKILL.md",
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"skills/hail-index/SKILL.md",
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"skills/hail-parallel-hpc/SKILL.md",
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"skills/hail-parallel-hpc/references/source_map.md",
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"skills/hail-test/SKILL.md",
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"skills/hail-theory-and-methods/SKILL.md",
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"skills/hail-theory-and-methods/references/doc_map.md",
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"skills/hail-troubleshooting/SKILL.md"
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],
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"deleted": [
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"skills/hail-parallel-hpc/SKILL.md",
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"skills/hail-parallel-hpc/references/doc_map.md",
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"skills/hail-parallel-hpc/references/source_map.md",
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"skills/hail-theory-and-methods/SKILL.md",
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],
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"modified": [
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"skills/hail-dev-docs/SKILL.md",
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"skills/hail-index/SKILL.md",
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"skills/hail-test/SKILL.md",
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"skills/hail-troubleshooting/SKILL.md"
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]
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},
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"skills/.compile_report.json",
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"skills/.evidence/memory.md"
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],
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"skills/hail-examples-and-tutorials/references/source_map.md",
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"skills/hail-test/SKILL.md",
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"skills/hail-test/references/doc_map.md",
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"skills/hail-test/references/source_map.md",
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"skills/hail-troubleshooting/SKILL.md",
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"skills/hail-troubleshooting/references/doc_map.md",
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"skills/hail-troubleshooting/references/source_map.md"
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],
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"deleted": [],
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"modified": [
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"skills/hail-build-and-install/references/source_map.md",
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"skills/hail-dev-docs/SKILL.md",
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"skills/hail-dev-docs/references/source_map.md",
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"skills/hail-examples-and-tutorials/SKILL.md",
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"skills/hail-examples-and-tutorials/references/doc_map.md",
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"skills/hail-examples-and-tutorials/references/source_map.md",
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"skills/hail-getting-started/SKILL.md",
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"skills/hail-getting-started/references/source_map.md",
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"skills/hail-index/SKILL.md",
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"skills/hail-simulation-workflows/references/source_map.md",
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"skills/hail-test/SKILL.md",
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"skills/hail-test/references/doc_map.md",
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"skills/hail-test/references/source_map.md",
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"skills/hail-troubleshooting/SKILL.md",
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"skills/hail-troubleshooting/references/doc_map.md",
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"skills/hail-troubleshooting/references/source_map.md"
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]
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}
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},
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"passes": [
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{
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"pass": 1,
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"return_code": 0,
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"status": "ok"
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},
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{
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"pass": 2,
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"return_code": 0,
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"status": "ok"
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},
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{
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"pass": 3,
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"return_code": 0,
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"status": "ok"
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}
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],
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"profile": {
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"docs_dirs": [
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"dev-docs",
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"hail/python/hail/docs",
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"hail/python/hailtop/batch/docs"
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],
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"docs_only": false,
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"notes": [
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"Monorepo layout; explicit roots avoid noisy auto-discovery of non-core lib/module folders.",
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"Primary end-user docs are under hail/python/hail/docs and hail/python/hailtop/batch/docs; dev-docs adds operator/developer workflows.",
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"Tutorial coverage combines notebook tutorials and Batch cookbook docs."
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],
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"package_name": "hail",
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"profile_path": "skills/.compile_profile.json",
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"profile_source": "file",
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"source_dirs": [
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"auth/auth",
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"batch/batch",
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"batch/jvm-entryway/src",
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"hail/hail/src",
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"hail/hail/ir-gen/src",
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"hail/hail/utils/src",
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"hail/python/hail",
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"hail/python/hailtop"
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],
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"test_dirs": [
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"auth/test",
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"batch/test",
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"ci/test",
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"monitoring/test",
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"hail/hail/test",
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"hail/python/test"
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],
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"tutorial_dirs": [
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"hail/python/hail/docs/tutorials",
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"hail/python/hailtop/batch/docs/cookbook"
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],
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"warnings": []
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},
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"project_root": "/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail",
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"run_id": "compile_20260304T212031220508Z",
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"skill_plan": {
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"available_skill_ids": [
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"hail-api-and-scripting",
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"hail-build-and-install",
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"hail-dev-docs",
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"hail-examples-and-tutorials",
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"hail-getting-started",
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"hail-index",
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"hail-inputs-and-modeling",
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"hail-parallel-hpc",
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"hail-simulation-workflows",
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"hail-test",
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"hail-theory-and-methods",
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"hail-troubleshooting"
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],
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"core_skill_ids": [
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"hail-api-and-scripting",
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"hail-test",
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"hail-build-and-install",
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"hail-getting-started",
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"hail-dev-docs",
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"hail-troubleshooting"
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],
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"deferred_gaps": [
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"Auto-discovery still over-selects some generic source roots in this monorepo; pass 2 should continue using explicit profile roots.",
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"Batch cookbook docs are explicit tutorial roots and may require manual weighting if topic clustering under-routes them.",
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"Large API docs volume may require post-generation consolidation to stay high-signal."
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],
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"goal": "Pass 2 builds high-impact docs-first Hail skills; pass 3 audits routing quality, source grounding, and coverage gaps.",
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"mode": "compile",
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"priority_skills": [
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{
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"action": "refresh",
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"must_cover": [
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"request triage across query, batch, install, and troubleshooting",
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"clear escalation order: primary docs -> doc_map -> source_map",
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"routing to tutorials and tests when users ask for runnable examples"
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],
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"reason": "Central router quality determines whether downstream answers stay docs-first and topic-correct.",
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"skill_id": "hail-index",
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"source_hints": [
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"skills/.compile_profile.json",
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"hail/python/hail/docs",
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"hail/python/hailtop/batch/docs",
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"dev-docs"
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]
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},
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{
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"action": "create",
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"must_cover": [
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"install/runtime prerequisites",
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"minimal first analysis workflow",
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"tutorial notebook entry points"
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],
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"reason": "Onboarding and first-run setup are frequent entry points and unblock most later requests.",
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"skill_id": "hail-getting-started",
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"source_hints": [
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"hail/python/hail/docs",
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"hail/python/hail/docs/tutorials",
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"hail/python/test"
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]
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},
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{
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"action": "create",
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"must_cover": [
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"local developer build paths",
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"package/component boundaries",
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"common build failures and fixes"
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],
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"reason": "Hail spans Python and JVM/service components, so build guidance is high-friction and high-impact.",
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"skill_id": "hail-build-and-install",
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"source_hints": [
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"dev-docs",
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"hail/hail/src",
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"hail/python/hail",
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"batch/jvm-entryway/src"
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]
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},
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{
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"action": "create",
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"must_cover": [
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"core query/table/matrixtable usage routes",
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"hailtop batch API usage and service/local backend patterns",
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"where to pivot from API docs to source for ambiguous behavior"
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],
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"reason": "Largest docs surface area; most user questions map to Python API and Batch scripting workflows.",
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"skill_id": "hail-api-and-scripting",
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"source_hints": [
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"hail/python/hail/docs",
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"hail/python/hailtop/batch/docs",
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"hail/python/hail",
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"hail/python/hailtop"
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]
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},
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{
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"action": "create",
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"must_cover": [
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"error triage checklist",
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"auth/cloud/runtime failure patterns",
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"test-backed sanity checks before deep source dives"
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],
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"reason": "Fast diagnosis patterns reduce repeated support loops for setup/runtime/auth/cloud issues.",
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"skill_id": "hail-troubleshooting",
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"source_hints": [
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"dev-docs/services",
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"hail/python/hail/docs/change_log.md",
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"hail/python/test",
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"hail/hail/test"
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]
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}
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],
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"version": 1,
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"warnings": []
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},
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"skill_plan_path": "skills/.evidence/skill_plan.json",
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"validation": {
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"core_skills_checked": [
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"hail-troubleshooting",
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"hail-test",
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"hail-simulation-workflows",
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"hail-getting-started",
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"hail-examples-and-tutorials",
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"hail-dev-docs"
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],
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"docs_only": false,
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"errors": [
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-troubleshooting/SKILL.md: playbook missing required element containing 'convergence/validation'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-test/SKILL.md: playbook missing required element containing 'convergence/validation'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-simulation-workflows/SKILL.md: playbook missing required element containing 'triage questions'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-simulation-workflows/SKILL.md: playbook missing required element containing 'pitfalls'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-simulation-workflows/SKILL.md: playbook missing required element containing 'convergence/validation'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-getting-started/SKILL.md: playbook missing required element containing 'convergence/validation'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-examples-and-tutorials/SKILL.md: playbook missing required element containing 'minimal working example'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-examples-and-tutorials/SKILL.md: playbook missing required element containing 'pitfalls'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-examples-and-tutorials/SKILL.md: playbook missing required element containing 'convergence/validation'.",
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"/mnt/home/taoeli/fermilink_repos/.fermilink-auto-compile/hail-hail/skills/hail-dev-docs/SKILL.md: playbook missing required element containing 'convergence/validation'."
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],
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"index_skills": [
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"hail-index"
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],
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"missing_planned_skills": [],
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"ok": false,
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"planned_skill_ids": [
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"hail-index",
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"hail-getting-started",
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"hail-build-and-install",
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"hail-api-and-scripting",
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"hail-troubleshooting"
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],
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"previous_source_inventory": {},
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"skills_total": 10,
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"source_inventory": {},
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"source_links_total": 80,
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"topic_skills": 9,
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"warnings": []
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}
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}

‎skills/.gitignore‎

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.evidence/

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