rename-project-research

name	rename-project-research
description	Use when you need to rename a research project across all systems (local directory, atlas, vault, Overleaf, git).
allowed-tools	Bash(mv*), Bash(ln*), Bash(ls*), Bash(readlink*), Bash(git*), Bash(find*), Bash(uv*), Read, Write, Edit, Glob, Grep, AskUserQuestion
argument-hint	[old-name new-name] or guided interview

Rename Research Project

Full project rename across all systems: local directory, atlas topic, vault (atlas + pipeline + submissions), Overleaf symlinks, git, and documentation. Replaces the old rename-atlas-slug skill with a complete pipeline.

When to Use

• Renaming a research project (directory, slug, or title)
• When the user says "rename project", "rename topic", "rename slug", "change project name"
• After deciding a project's working title should change
• When merging two projects (rename one to match the other)

Input

Parameter	Format	Required
Old name	Project name, slug, or directory name	Yes
New name	Project name, slug, or directory name	Yes

If the user provides natural-language names, derive:

• Slug (kebab-case): new-project-name
• Directory name (Title Case): New Project Name
• Display title (natural): New Project Name

Confirm all three forms before proceeding.

Processing Steps

Phase 1: Verify and Plan

1. Resolve old project — find the atlas topic file:

   TM="$(cat ~/.config/task-mgmt/path)"
   grep -rl "project_path:.*<old-basename>" ~/vault/atlas/ 2>/dev/null
   

   If not found, search by slug: find ~/vault/atlas/ -name "<old-slug>.md"

2. Read atlas topic — extract: theme, title, project_path, outputs, connected_topics

3. Locate project directory — resolve from project_path: field:

   RESEARCH_ROOT="$(cat ~/.config/task-mgmt/research-root)"
   ls -d "$RESEARCH_ROOT/<project_path>" 2>/dev/null
   

4. Inventory what needs renaming:

   System	What to check
   Local directory	$RESEARCH_ROOT/<theme>/<Old Name>/
   Atlas topic file	~/vault/atlas/<theme>/<old-slug>.md
   Atlas connected_topics	All topic files referencing old slug
   Vault theme file	~/vault/themes/{theme-slug}.md (verify topic_count if maintained)
   Atlas paperpile.md	Folder reference
   Project CLAUDE.md	Title, slug, any self-references
   Project README.md	Title
   Project MEMORY.md	Title in header
   Project .context/	current-focus.md, project-recap.md titles
   vault atlas entry	Name, Atlas Slug property
   vault submission entries	Submission name
   Paper directories	Overleaf symlink targets (may need new Overleaf project names)
   Backup directory	backup/ subdirectory names
   TM _index.md	Project row in Papers in Progress table
   TM current-focus.md	Any references to old name
   Git	No rename needed (repo stays at same path after dir rename)

5. Present plan — show the full rename map and wait for confirmation.

Phase 2: Atlas Rename (Steps 1–11 from old rename-atlas-slug)

2.1 Rename topic file

mv ~/vault/atlas/{theme}/{old-slug}.md ~/vault/atlas/{theme}/{new-slug}.md

2.2 Update YAML frontmatter

In the renamed file, update:

• title: → new display title
• project_path: → <theme>/<New Directory Name>
• Leave other fields unchanged

2.3 Update connected_topics (all files)

Grep all topic files for old slug in connected_topics arrays. Replace exact matches only.

2.4 Verify theme directory

The topic file is already in the correct theme directory after the rename in 2.1. No separate slug list to update — themes are individual files at ~/vault/themes/.

2.5 Update paperpile.md

Rename folder entry if present.

2.6 Update merge-reviewed.md

Replace old slug if present. Skip if file doesn't exist.

2.7 Check prose references

Grep all topic bodies for prose mentions of old slug. Update found references.

2.8 Regenerate RECAP.md

uv run python packages/atlas-vault/generate_recap.py

2.9 Verify atlas clean

Grep entire packages/atlas-vault/ for remaining old slug references.

Phase 3: Local Project Rename

3.1 Rename directory

mv "$RESEARCH_ROOT/<theme>/<Old Name>" "$RESEARCH_ROOT/<theme>/<New Name>"

3.2 Update project CLAUDE.md

• Title heading
• **Slug:** field
• Any self-references in text

3.3 Update project README.md

• Title heading

3.4 Update project MEMORY.md

• Header: # Knowledge Base — <New Name>

3.5 Update project .context/

• current-focus.md title
• project-recap.md title

3.6 Update Overleaf symlinks

For each paper*/paper symlink, check if the target path contains the old name:

for link in paper*/paper; do
  target="$(readlink "$link")"
  if [[ "$target" == *"<Old Name>"* ]]; then
    echo "⚠ Symlink $link points to target containing old name: $target"
    echo "  Overleaf project may need manual rename in Overleaf UI"
  fi
done

Do NOT rename Overleaf folders — renaming loses Overleaf project history. The user must rename via the Overleaf UI. Flag as manual TODO and only update the symlink after the user confirms the rename is done.

3.7 Git re-init (if needed)

If git repo was at old path, it moves with the directory. No action needed unless there's a remote with the old name.

Phase 4: Vault Rename

4.1 Find and update topic entry

# Search for topic
# Use `taskflow-cli search-tasks --query "<old-name>" --json` to find, then edit the vault markdown file directly
curl -s -X PATCH "https://vault file edit (~/vault/)/<topic-id>" \
  # vault files are local — no auth needed \
  -H "Content-Type: text/markdown" \
  -H "Content-Type: application/json" \
  -d '{"properties": {"Name": {"title": [{"text": {"content": "<New Name>"}}]}, "Atlas Slug": {"rich_text": [{"text": {"content": "<new-slug>"}}]}}}'

4.2 Update submission entries

For each submission entry, update the Submission name if it contains the old name.

Phase 5: Task Management Updates

5.1 Update _index.md

Find and update the project row in .context/projects/_index.md.

5.2 Update current-focus.md

Replace old project name references in .context/current-focus.md.

5.3 Update papers context file

Rename .context/projects/papers/<old-name>.md → <new-name>.md if it exists. Update title inside.

5.4 GitHub artifact repo rename (with anonymous-URL safety check)

If <project>/github-repo/ exists with a GitHub remote whose name embeds the old slug:

1. Check for live anonymous URLs — read the matching vault submission frontmatter at ~/vault/submissions/<old-slug>-<venue>-<year>.md (and any other submissions for this paper). Look for anonymous_repo:.

2. If anonymous_repo: is set:

   • The 4open.science URL is immutable and embeds the GitHub repo's old name. Renaming the GitHub repo would break the anonymous mirror — reviewers may currently be reading it.
   • Default behaviour: skip the GH rename. Print a warning explaining the trade-off and leave the existing GH repo + 4open.science mirror untouched.
   • Prompt the user with three options: (a) skip GH rename (default), (b) rename anyway and accept that the 4open.science URL will break — useful only if reviewing is over and the mirror is no longer needed, (c) defer the rename until after a future re-submission cycle creates a new artifact under the new name.

3. If no anonymous_repo: is set (no double-blind submission active):

   • Rename via gh repo rename user/<old-repo-name> <new-repo-name> from inside github-repo/.
   • Update github-repo/.git/config remote URL (gh handles this automatically when gh repo rename runs locally).
   • Naming follows whichever mode applies: Mode A (<venue>-<year>-<new-slug>-artifact) or Mode B (paper-<theme>-<new-slug>). See init-project-research/references/github-release-repo.md.

4. Update vault submission artifact_repo: field to the new GitHub URL. Atlas outputs[].artifact_repo: likewise. Same atomicity rule as /anonymous-artifact Phase 6 — apply all writebacks together or none.

Phase 6: Verification

1. Grep for old name across all systems:

   grep -r "<old-slug>" "$TM/packages/atlas-vault/" 2>/dev/null
   grep -r "<Old Name>" "$RESEARCH_ROOT/<theme>/<New Name>/" 2>/dev/null
   grep -r "<old-slug>\|<Old Name>" "$TM/.context/" 2>/dev/null
   

2. Report remaining references that couldn't be auto-fixed.

3. List manual TODOs:

   • Overleaf project rename (if symlink targets contain old name)
   • Paperpile/Paperpile folder rename on Google Drive
   • Any external references (email threads, shared docs)

Anti-Patterns

• Do NOT rename Overleaf folders — this destroys project history. User must rename via Overleaf UI
• Do NOT rename Paperpile folders automatically — flag as manual TODO
• Do NOT edit RECAP.md directly — always regenerate via script
• Do NOT use Edit without first reading the file
• Do NOT do partial slug matches — "old-slug" must match exactly
• Do NOT proceed without confirmation after presenting the plan
• Do NOT strip references to the renamed project from other atlas topics, vault submissions, or context files. Rename the symlink and target to the new name; inbound references must be updated to the new name, never removed. Deleting references breaks the reference graph and loses history. If a reference seems redundant, flag it for manual review — do not delete.

Output

After completion, report:

Project renamed: <Old Name> → <New Name>

Systems updated:
  Atlas topic file:    ✓ renamed + frontmatter updated
  Atlas cross-refs:    ✓ N files updated
  Theme directory:     ✓ verified
  Local directory:     ✓ renamed
  Project CLAUDE.md:   ✓ title + slug updated
  Project README.md:   ✓ title updated
  Vault atlas:        ✓ Name + Atlas Slug updated
  Vault submissions:  ✓ N entries updated
  TM _index.md:        ✓ row updated
  TM current-focus.md: ✓ references updated
  RECAP.md:            ✓ regenerated

Manual TODOs:
  - [ ] Rename Overleaf project(s) in Overleaf UI
  - [ ] Rename Paperpile folder on Google Drive

Remaining references: [list or "none"]

Cross-References

Skill	Relationship
/audit-project-research	Run after rename to verify structure
/session-close	Atlas cross-ref check will validate the rename
vault sync (edit vault files directly)	Can be used for follow-up vault sync if needed
/sync-atlas	Can be used for follow-up atlas-vault sync