research-context-compressor

Build a compact, machine-readable workspace memory at the project root under .research/. Other research-hub skills (project-orienter, literature-triage-matrix, paper-memory-builder) read these files instead of rescanning the repo every session, which is where the token savings come from.

This is the foundation skill. Run it once per project and refresh when the project's research question, datasets, or experiment set changes.

When to use

Trigger phrases:

• "Compress this project context for future agents."
• "Create a research manifest so future sessions don't reread everything."
• "Save the key project context before we continue."
• "Build a .research/ folder for this repo."

Not for:

• Compressing source code or generating doc strings — that's a code task.
• Running experiments or analyzing results — those write to outputs/, not .research/.
• Writing the manuscript itself.

Inputs you should read (whichever exist — priority order)

The compressor reads whatever your project has. None of these are required. If a file is missing, that field of the manifest stays empty (see "What NOT to do"). Skim, do not deep-read.

For any project:

1. README.md at the repo root — project overview. Single most useful input.
2. .research/design_brief.md if it exists — Stage 3a handoff from research-design-helper (plugin v0.3.12+). Read the frontmatter (project, source, gap_verdict) plus section 1 (Research question) only — informs the project_manifest.yml research_question field. The brief is the authority on the sharpened RQ; the manifest mirrors it. Don't deep-read; skim. If frontmatter source: topic_dossier.gaps.yml#<id> is set, copy that gap-id into the manifest's provenance.from_gap field (forward-compat with the Stage 2 → 3a wire).

For code-based research projects (Python / JS / R / Julia / etc.):

3. pyproject.toml / package.json / requirements.txt / renv.lock / Project.toml — primary tools.
4. scripts/ and notebooks/ — main entrypoints.
5. data/ and outputs/ — datasets and artifacts.

For qualitative / archival / interpretive projects:

3. notes/, drafts/, sources/ — manuscript-track work.
4. .obsidian/ — Obsidian vault settings, if present.
5. Any plain-text bibliography file (bibliography.md, sources.bib, references.json).

For both:

6. docs/ — long-form descriptions.
7. .git/HEAD and git log --oneline -20 — current branch + recent activity, if a git repo.
8. .research/ (if it already exists) — for refresh, not first-time create.

An empty manifest field is better than an invented one.

For a worked humanities-project example with minimal scaffold (README + notes/ only, no code, no data/), see references/example-humanities-project.md. It illustrates the "empty fields are honest" rule.

Outputs you must produce

Write these to <project-root>/.research/:

• project_manifest.yml — top-level orientation. Required.
• experiment_matrix.yml — per-experiment status. Required if scripts/ or notebooks/ exist.
• data_dictionary.yml — datasets and schemas. Required if data/ exists.
• run_log.md — append a single entry recording this run.
• decisions.md — leave empty if no ADRs yet; do not invent decisions.
• open_questions.md — list any obvious unknowns you spotted (e.g. undocumented dataset, missing license, ambiguous entrypoint).

Stage 2 → 3a provenance (v0.3.13+). If .research/design_brief.md exists AND its frontmatter sets source: topic_dossier.gaps.yml#<gap-id>, copy that pointer into the project_manifest.yml provenance.from_gap field as part of every write:

# project_manifest.yml — minimal example showing the v0.3.13 provenance wire
project_name: "..."
research_question: |
  ...  # mirrored from design_brief.md §1 (sharpened RQ)
current_stage: "design"
last_updated: "YYYY-MM-DD"
provenance:
  from_gap: "topic_dossier.gaps.yml#G2"   # exact copy of design_brief frontmatter `source`

If no design_brief.md exists or its frontmatter source field is empty, omit the provenance: block entirely — do NOT write provenance: {} or provenance: null. The schema doc (docs/research-workspace-manifest.md) records the field as optional; absent is the honest state when the upstream chain isn't connected.

If a file already exists, update don't replace: keep human-edited fields, fill in only the empty ones unless the user said "regenerate from scratch". This rule also applies to provenance.from_gap — if a manifest already has provenance.from_gap and the current design_brief.md source differs, ask the user before overwriting (matches the v0.3.12 provenance-protection logic in research-design-helper).

Schema reference

Full schema lives in docs/research-workspace-manifest.md. Quick reminder of project_manifest.yml required fields:

• project_name
• research_area
• research_question
• current_stage (one of discovery / exploration / experiments / writing / rebuttal / submission)
• last_updated (today's date in ISO format)

If you don't know a field, leave it empty ("" or []). Do not guess research questions, hypotheses, or claims.

Token-saving behavior

• Read manifest files first if they exist; only inspect code/data when the manifest doesn't already cover what you need.
• For large directories, list contents and pick representative entrypoints rather than reading every file.
• After running, tell the user: "Wrote .research/project_manifest.yml (and N other files). Future agents loading the research-project-orienter skill can now orient themselves without re-reading the whole repo."

Output format for the user

After writing the files, print a 5-line summary:

[research-context-compressor]
  Wrote: .research/project_manifest.yml (3 datasets, 2 entrypoints)
  Wrote: .research/experiment_matrix.yml (2 experiments)
  Wrote: .research/data_dictionary.yml (3 datasets)
  Open questions surfaced: 2 — see .research/open_questions.md
  Refresh later: ask "compress this project context" again.

What NOT to do

• Don't write to .paper/ — that's paper-memory-builder's job.
• Don't write .research/literature_matrix.md — that's literature-triage-matrix's job.
• Don't write to .research_hub/ — that's research-hub's internal cache, managed by the CLI.
• Don't invent fields not in the schema. Add a line to .research/open_questions.md instead.
• Don't overclaim: if the project has no clear research question yet, leave research_question empty and add a question to open_questions.md.

See also

• references/example-humanities-project.md — worked example for a non-code research project (minimal scaffold)