refactor(autoresearch): consolidate outputs into .autoresearch/ directory

[baleen37]

Summary

Move all autoresearch plugin output files from project root into .autoresearch/ directory to reduce root clutter.

Changes

• Update hook script to check .autoresearch/autoresearch.md and .autoresearch/off instead of root-level paths
• Update command file to use .autoresearch/ paths for all file operations (off sentinel, resume, fresh start)
• Update skill file to use .autoresearch/ paths throughout (setup, JSONL protocol, running, logging, dashboard, loop rules, ideas backlog)
• File mapping: autoresearch.md → .autoresearch/autoresearch.md, autoresearch.sh → .autoresearch/run.sh, autoresearch-dashboard.md → .autoresearch/dashboard.md, experiments/worklog.md → .autoresearch/worklog.md, autoresearch.ideas.md → .autoresearch/ideas.md, .autoresearch-off → .autoresearch/off

Tests

• All 63 BATS tests pass
• Verified no stale paths remain via grep
• Bash syntax validation on hook script passes

Summary by CodeRabbit

• Refactor

  • Consolidated autoresearch plugin outputs into a dedicated .autoresearch/ directory, moving all session artifacts, dashboards, logs, and state files from scattered root-level and experiment folder locations for improved project organization.

• Documentation

  • Added design specification and consolidation plan documentation detailing the autoresearch directory restructuring implementation strategy.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 7be9d728-75e6-4bc6-9f04-a236f07c6b38

📥 Commits

Reviewing files that changed from the base of the PR and between 9f144aa and 2768ed8.

📒 Files selected for processing (5)

• docs/superpowers/plans/2026-03-27-autoresearch-dotdir.md
• docs/superpowers/specs/2026-03-27-autoresearch-dotdir-design.md
• plugins/autoresearch/commands/autoresearch.md
• plugins/autoresearch/hooks/autoresearch-context.sh
• plugins/autoresearch/skills/autoresearch/SKILL.md

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📝 Walkthrough

Walkthrough

This PR consolidates all autoresearch plugin outputs into a dedicated .autoresearch/ directory. Files previously scattered across the project root and nested folders are relocated with accompanying path updates in the command handler, context hook, and skill documentation. Two design and planning documents define the consolidation strategy and specific implementation details.

Changes

Cohort / File(s)	Summary
Documentation & Planning docs/superpowers/plans/2026-03-27-autoresearch-dotdir.md, docs/superpowers/specs/2026-03-27-autoresearch-dotdir-design.md	New spec and plan documents detailing the consolidation of autoresearch outputs into .autoresearch/ directory, including state file mappings, detection rules, and affected plugin files.
Plugin Implementation plugins/autoresearch/commands/autoresearch.md, plugins/autoresearch/hooks/autoresearch-context.sh, plugins/autoresearch/skills/autoresearch/SKILL.md	Updated plugin files to use new .autoresearch/ paths for state files, configuration, logs, and dashboard. Includes directory creation logic, path checks in resumption conditions, and command references.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Poem

🐰 Scattered files from far and wide,
Now nestle in a burrow with pride!
Into .autoresearch/ they go,
Organized, tidy, and all aglow—
A rabbit's dream of harmony, you know! ✨

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch refactor/autoresearch-dotdir

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