Autosci Reset

/reset

Resets the wiki to a clean scaffold by scope. Designed for development iteration and recovery after a failed setup — not a routine operation.

Trigger

Manual: /reset --scope wiki / --scope raw / --scope log / --scope checkpoints / --scope all. Multiple scopes may be combined comma-separated: --scope wiki,log.

Inputs

• --scope (required): one of
  • wiki — delete every *.md under wiki/<entity>/ and wiki/outputs/, plus wiki/index.md, wiki/log.md, and wiki/graph/ files. Preserves .gitkeep and wiki/CLAUDE.md.
  • raw — delete every entry under raw/papers/, raw/discovered/, raw/tmp/, raw/notes/, raw/web/ (except .gitkeep).
  • log — reset wiki/log.md to the empty header.
  • checkpoints — clear batch state via research_wiki.py checkpoint-clear.
  • all — every scope above.

Outputs

• Cleared / reset files on disk.
• Console summary of deleted files and reset files.

Wiki Interaction

Reads

• All wiki/<entity>/*.md (to enumerate the deletion plan).
• raw/<sub>/* (to enumerate raw deletions).

Writes

• Deletes wiki/<entity>/*.md (preserves .gitkeep).
• Rewrites wiki/index.md, wiki/graph/*, optionally wiki/log.md.
• Deletes raw/<sub>/* (except .gitkeep).

Workflow

Pre-conditions: working directory contains wiki/, tools/. Set WIKI_ROOT=wiki/.

Step 1: Build the deletion plan (dry-run)

python3 tools/reset_wiki.py --scope <scope>

This prints a JSON plan listing every file that would be deleted or reset, without modifying anything. Display the plan to the user grouped by scope (wiki entity dirs, raw subdirs, log, checkpoints).

Step 2: Confirm with the user

Print the plan summary and ask for explicit confirmation:

About to delete N files and reset M files. Continue? [y/N]

If the user says no, exit. Never proceed without explicit approval — /reset is destructive and raw/ deletions are not tracked by git.

Step 3: Execute

python3 tools/reset_wiki.py --scope <scope> --yes

The tool prints a JSON status report ({deleted_files, reset_files}).

Step 4: Log (unless log scope was reset)

If the executed scope did not include log, append a log entry so future sessions can see the reset happened:

python3 tools/research_wiki.py log wiki/ "reset | scope: <scope>"

Step 5: Report

Print the result and suggest next steps:

## Reset complete — scope: <scope>

Deleted: N files
Reset:   M files

Next steps:
- /init       — bootstrap wiki from raw/
- /prefill    — seed foundational background
- /ingest     — add a single source manually

Constraints

• Confirm before destructive action: never call --yes without showing the plan and asking the user.
• Preserves: .gitkeep placeholders, wiki/CLAUDE.md, .claude/ (skills are never touched).
• raw/ deletes are irreversible: PDFs are not in git history. Warn the user before executing raw or all scopes.
• /reset does not touch tools/, mcp-servers/, i18n/, .env, or git state.
• Scope is required: no default action (/reset with no flag prompts for scope rather than guessing).

Error Handling

• Unknown scope: print valid scopes and exit nonzero.
• Missing wiki directory: report and suggest running /init.
• checkpoint-clear failure: log a warning but do not fail other scopes.

Dependencies

Tools (via Bash)

• python3 tools/reset_wiki.py --scope <scope> [--yes] [--project-root .] — deterministic destructive helper
• python3 tools/research_wiki.py log wiki/ "<message>" — append log
• reset_wiki.py clears wiki/.checkpoints/*.json directly for checkpoints scope (no CLI dispatch — the checkpoint-clear subcommand requires a specific task_id, while /reset --scope checkpoints semantics is "clear everything")