refactor: shared agent workflows (F01) and one application registry (F02)
Checkpoint for the 2026-09-11 project review remediation. Work by a previous agent that ran out of context; committed unchanged as a rollback point before the remaining findings land on top of it. F01 — the two agent directories had drifted into different processes - Six shared workflows under `resume_builder/reference/workflows/`; both `.agents/skills/` and `.claude/skills/` are now thin entrypoints that route to the same file instead of carrying full copies. - The `.claude` copies were the stale side: fixed bullet line variants and character budgets that the newer process had already dropped. Removing them is the point of the change, not collateral. - Parity/link regression test added; corrected the top-level file map, which pointed at a directory that does not exist. F02 — application status was stored in four places and disagreed - New registry `job_scout/state/applications.json` (26 records) with `application_records.py` (schema, validation, transactional write) and `application_tracker.py` (add/update, no quota). - AGENTS.md and CLAUDE.md no longer keep their own status tables; both point at `current_applications.md`, generated from the registry. - Interview-reached is now independent of outcome, so a withdrawal after an interview can record both facts. The old tables are preserved verbatim in `job_scout/state/history/application_status_before_2026-09-11.json`. Verification: `python -m unittest discover -s tests -v` — 18/18 pass. Spot-checked that the detailed SBB and Kdo Cy notes survived the migration into the registry rather than being flattened. Known unresolved, deliberately not invented (see FIX_PROGRESS.md): Aker BP's application date and its Adjacent-despite-79 classification. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Qej5SBvhcbGXHwLqNWiskM
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---
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description: Extract structured information from research papers, PDFs, or code into knowledge base extractions
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name: setup-extract
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description: Extract source-grounded career evidence from papers, employment records, project documents, and notes into structured knowledge-base files without promoting inference to fact.
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user-invocable: true
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---
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# /setup-extract
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# Shared project workflow
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**User input:** `$ARGUMENTS`
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Read and follow [the setup-extract workflow](../../../resume_builder/reference/workflows/setup-extract.md) before doing this task. Resolve project paths from the repository root.
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Parse `$ARGUMENTS`:
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- File path to a paper (e.g., `papers/Smith2024_catalyst.pdf`, `papers/project_report.tex`) → read that file
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- Multiple paths separated by spaces → batch mode (process each sequentially)
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- Empty → ask the user for the paper path or paste content
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---
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## Startup
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1. Read `CLAUDE.md` — check KB Corrections Log for known issues
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2. Read `config.md` — load Personal Info (to identify user's author position), Provenance Flags
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3. Read `knowledge_base/extractions/_INVENTORY.md` — see what's already extracted, avoid duplicates
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If the paper is already in the inventory:
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- Show the existing extraction path
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- Ask: "This paper is already extracted. Re-extract (overwrite) or skip?"
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- Wait for user response before proceeding
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---
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## Phase 1: Read & Understand the Paper
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Read the paper using the appropriate method:
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- **PDF files:** Use the Read tool (supports PDF reading)
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- **.tex source:** Read directly — often has more detail than the compiled PDF
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- **If both exist:** Prefer .tex for content extraction, use PDF for figures/tables
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**While reading, collect:**
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1. Full title, all authors, year, journal/venue, DOI (if available)
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2. The user's position in the author list (first, co-first, second, middle, last, corresponding)
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3. Publication status (check `config.md` Provenance Flags first, then infer: published / under review / draft / internal)
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4. All computational methods, experimental techniques, software, and frameworks mentioned
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5. Quantitative results — speedups, accuracies, efficiencies, improvements over baselines
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6. Novelty claims — "first-ever", "new framework", "novel approach", etc.
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7. Collaboration indicators — other groups, institutions, shared resources
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8. Funding acknowledgments
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Progress: "Reading paper... [title] by [first author] et al., [year]"
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---
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## Phase 2: Clarify User's Role
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If the user's contribution is not obvious from the paper (common for multi-author work), ask:
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**Questions to ask (skip any that are already clear from the paper):**
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1. "What was your specific contribution? (e.g., all computational work, specific analysis, code development)"
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2. "Did you develop any tools, methods, or code used in this paper?"
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3. "Were there other groups or institutions involved? What was your group's role?"
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4. "Any quantitative results you can personally claim? (e.g., 'I ran all the simulations')"
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5. "Is there anything in this paper that should NOT appear on your resume? (e.g., collaborator's experimental data)"
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### >>>>>> MANDATORY STOP — DO NOT PROCEED <<<<<<
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Present your understanding of the paper and ask the clarifying questions above.
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**You MUST wait for the user's explicit text response before continuing.**
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---
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## Phase 3: Write Extraction
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Create the extraction file at `knowledge_base/extractions/<AuthorYear_short_descriptor>.md`
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**Naming convention:** `<FirstAuthorLastName><Year><2-3_word_descriptor>.md`
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- Examples: `Smith2024_protein_stability.md`, `Chen2023_binding_affinity.md`
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- If the user is first author: use their last name
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- Normalize to lowercase with underscores
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**Extraction format:**
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```markdown
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# [Full Paper Title]
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## Metadata
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- **Authors:** [author list — highlight user's name with bold]
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- **Year:** [year]
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- **Journal:** [journal/venue or "unpublished"/"internal"/"under review at X"]
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- **DOI:** [DOI or "N/A"]
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- **User's role:** [first author / co-first / contributing / corresponding]
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- **Status:** [published | under review | draft | internal]
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## Methods & Tools
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- **Computational methods:** [e.g., MD, ML, FEA, CFD, etc. — be specific about methods, force fields, etc.]
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- **Software/frameworks:** [e.g., GROMACS, PyTorch, ABAQUS, custom code, etc.]
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- **Hardware/HPC:** [if mentioned — clusters, GPU resources, etc.]
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- **Key techniques:** [specific methodological details that map to resume skills]
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## Key Results
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[Number each result. Include quantitative metrics wherever possible.]
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1. [Result with numbers — e.g., "Achieved 5,000x speedup over brute-force screening"]
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2. [Result — e.g., "Screened 8,500 variants, identified 7 top candidates"]
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3. [...]
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## Novelty Claims
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[What's genuinely new — be precise, avoid overclaiming]
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- [e.g., "First application of framework X to system Y"]
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- [e.g., "New method combining A and B — no prior work exists"]
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## Collaboration & Scope
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- **Other groups:** [institutions, PIs involved]
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- **User's specific contribution:** [from Phase 2 clarification]
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- **Shared vs. sole work:** [what the user did alone vs. with others]
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## Provenance Notes
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- **Publication status:** [matches config.md if listed there]
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- **Safe to claim:** [what the user can put on a resume without hedging]
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- **Needs hedging:** [claims that require "contributed to" or "supported" framing]
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- **Do NOT claim:** [results from collaborators, claims that would be overclaiming]
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## Resume Bullet Seeds
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[3-5 draft bullets in STAR format. These are seeds, not final text.]
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[Use full-ownership verbs only for sole-contributor work. Hedge for shared work.]
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1. [Action verb] + [what was done] + [quantitative result/impact]
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2. [Action verb] + [method/tool developed] + [what it enabled]
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3. [Action verb] + [scope — e.g., "across N systems"] + [outcome]
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4. [Optional: collaboration-framed bullet]
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5. [Optional: tool/infrastructure bullet]
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```
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Save the file. Show the user the complete extraction.
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Progress: "Writing extraction for [short title]... [N] results identified, [M] bullet seeds drafted"
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---
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## Phase 4: Update Inventory
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Read and update `knowledge_base/extractions/_INVENTORY.md`.
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Add a row to the inventory table:
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```
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| [filename] | [short title] | [user's role] | [status] | [primary methods] | [date extracted] |
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```
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Present the updated inventory entry to the user.
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---
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## Phase 5: Next Steps
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After extraction is complete, present:
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1. **Extraction summary:** [N] methods, [M] quantitative results, [K] bullet seeds
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2. **Provenance flags:** Any items that need special handling
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3. **Suggested next action:**
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- If more papers to extract: "Run `/setup-extract [next paper path]`"
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- If all papers done: "Run `/setup-build-kb` to synthesize extractions into experience files and bundles"
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### >>>>>> MANDATORY STOP <<<<<<
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Present extraction summary. Wait for user feedback or next paper.
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**You MUST wait for the user's explicit text response before continuing.**
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---
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## Batch Mode
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If `$ARGUMENTS` contains multiple file paths:
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1. Process each paper through Phases 1-4 sequentially
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2. Ask Phase 2 clarifying questions for ALL papers at once (grouped) before writing any extractions
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3. After all extractions: present combined inventory update and summary
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4. Single STOP at the end (not per paper)
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This shared file is the only workflow implementation for both agents. Preserve existing user authorization and resume from the application's recorded state.
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