Initialize a missing research Workspace from the repository template without overwriting existing Run state; use before Pipeline binding when the target under `workspaces/` has no valid core artifacts.
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See how to installReview the instructions the agent will receive before you install.
Initialization is a boundary: it creates Workspace-owned state and leaves existing state untouched unless overwrite is an explicit operator decision. It does not select a Workflow or execute a Unit.
workspaces/<name>/.STATUS.md, CHECKPOINTS.md, UNITS.csv, and DECISIONS.md.GOAL.md and queries.md.papers/, outline/, citations/, and output/ directories.Resolve the target path and reject the repository root. Inspect existing files before deciding whether initialization is missing, partial, or already complete. Never infer overwrite permission from a partial Workspace.
Completion criterion: the destination is a Workspace path and every existing file that could be replaced is known.
Copy the repository-owned template into the target. Default to create-missing;
use --overwrite only after an explicit replacement decision.
Completion criterion: all missing base files and directories are materialized, and no pre-existing file was replaced without explicit permission.
Confirm that STATUS.md, UNITS.csv, CHECKPOINTS.md, and DECISIONS.md
exist. Parse the UNITS.csv header and reject malformed CSV rather than
leaving a superficially initialized Workspace.
Completion criterion: the four core files exist and UNITS.csv has the
required schema.
Leave Workflow selection and Pipeline-specific Unit materialization to
pipeline-router or the Pipeline adapter. The generic template is not evidence
that a Goal has been routed.
Completion criterion: the Workspace can be passed to the router without requiring any state from chat history.
assets/workspace-template/ only when inspecting or changing the base
template contract.pipelines/*.pipeline.md only after Workflow binding.research-pipeline-runner when the user asked to continue beyond
initialization.uv run python .codex/skills/workspace-init/scripts/run.py \
--workspace workspaces/<name>
--workspace <path>: target Workspace.--overwrite: replace existing template-owned files after explicit approval.--unit-id, --inputs, --outputs, --checkpoint: Pipeline-runner
compatibility arguments.Inspect the interface before use:
uv run python .codex/skills/workspace-init/scripts/run.py --help
Replace template files only after an explicit reset decision:
uv run python .codex/skills/workspace-init/scripts/run.py \
--workspace workspaces/<name> \
--overwrite
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Internal template for creating or refactoring a skill into the repository's reference-first shape. **Trigger**: reference-first template, blueprint skill, create a reusable skill, refactor a script-heavy skill. **Use when**: you need a lean `SKILL.md`, explicit `references/`, machine-readable `assets/`, and a minimal deterministic `run.py`.
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Download a small corpus of open-access arXiv survey/review PDFs about agentic systems and extract text for style learning.
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Extract per-subsection “anchor facts” (NO PROSE) from evidence packs so the writer is forced to include concrete numbers/benchmarks/limitations instead of generic summaries.
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Curate reader-facing survey tables for the Appendix (clean layout + high information density), using only in-scope evidence and existing citation keys.
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Build a final, machine-readable argument snapshot from current H3 sections and refresh section fingerprints before merge.
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Audit one research Workspace for declared Unit outputs and Pipeline target Artifacts, writing `output/CONTRACT_REPORT.md`; use for mid-Run coverage snapshots or final delivery completeness, not deep provenance integrity.
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