merge-projects

name	merge_projects
description	Identify overlapping projects and merge them into consolidated notes

🔀 Merge Projects Skill

Detect overlapping or closely related projects and merge them into a single consolidated project note.

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CRITICAL RULES

• Never merge automatically — always present candidates and get user approval
• Never delete source projects until merged project is verified
• Merged project inherits the highest status of its sources (seed < idea < active < writing < finished)
• All paper links from source projects must be preserved in merged project
• All MOC links from source projects must be preserved in merged project
• Bidirectional links must be updated: papers that linked to old projects must link to merged project
• Vault index must be updated after merge

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WORKFLOW

1. Choose mode

Ask user:

• Scan for candidates? (analyze all projects for overlap)
• Merge specific projects? (user names 2-3 projects to merge)

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2a. Scan mode — Identify merge candidates

Read vault index to get all projects and their descriptions.

For each project pair, assess overlap signals:

• Similar research questions or hypotheses
• Shared relevant papers (≥2 papers in common)
• Overlapping MOC links
• Complementary seed ideas (one project's approach is another's variant)
• Same phenomenon studied from slightly different angles

Score overlap:

• 🔴 High overlap (likely should merge): same core question, ≥3 shared papers, nearly identical hypotheses
• 🟡 Moderate overlap (consider merging): related questions, 2 shared papers, one could be a variant of the other
• 🟢 Low overlap (keep separate): distinct questions, ≤1 shared paper, different mechanisms

Present candidates grouped by overlap score. For each candidate pair/group:

• List the projects
• Explain WHY they overlap (shared papers, similar questions, etc.)
• Suggest which project should be the "primary" (the more developed one)
• Suggest a merged title if current titles are too narrow

Get user approval before proceeding to merge.

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2b. Direct merge mode — User specifies projects

• Read all specified project files in full
• Confirm overlap is real
• Ask user which should be primary (or suggest based on development level)
• Proceed to merge

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3. Execute merge

Create merged project:

• Use the primary project as base
• Integrate content from secondary project(s) section by section:

Section	Merge strategy
Current Focus	Keep primary's; note secondary's angle if distinct
Seed Idea	Combine triggers from all sources
Current Working Idea	Synthesize into broader framing
Research Question	Merge into unified question; keep sub-questions if distinct
Hypothesis / Claim	Keep primary; add secondary as alternative hypothesis if different
Context & Motivation	Union of all motivations
Possible Approaches	Union of all approaches (deduplicate)
Research Ideas & Variants	Secondary project's main direction becomes a variant
Related Work	Union (deduplicate)
Relationship to Prior Work	Union (deduplicate)
Possible Experiments	Union (deduplicate)
Open Questions & Risks	Union (deduplicate)
Next Actions	Union; remove completed/redundant
Relevant Papers	Union of ALL paper links (no paper lost)

Decide on merged title:

• If primary title is broad enough → keep it
• If both titles are narrow → create new title capturing combined scope
• Title must be concise and descriptive

Set merged status:

• Use highest status among source projects
• If any source is active or higher → merged project inherits that status

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4. Update all references

Papers linking to absorbed projects:

• Find all papers in Reading/ that link to secondary (absorbed) project(s)
• Replace [[Old Project Name]] with [[Merged Project Name]] in their "Linked Research Projects" section

MOCs containing absorbed projects:

• Find MOCs listing secondary project(s)
• Replace with merged project link (avoid duplicates if primary already listed)

Projects referencing absorbed projects:

• Check if any other projects reference the absorbed ones in Related Work
• Update those references

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5. Remove absorbed projects

Only after verification:

• Confirm merged project file exists and is complete
• Confirm all paper links updated
• Confirm all MOC links updated
• Confirm no remaining references to old project names

Then delete secondary (absorbed) project files.

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6. Update vault index

• Run update_vault_index logic or notify user to run /update_vault_index

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TOKEN EFFICIENCY

Optimizations:

• In scan mode: read only vault index + project frontmatter + Relevant Papers sections first
• Only read full project files for confirmed merge candidates
• Use grep to find references to absorbed project names across vault
• Batch reference updates per file

Avoid:

• Reading all project files in full during scan phase
• Reading paper files unless needed for reference updates
• Multiple passes over same files

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OUTPUT RULES

• Scan results: table of candidate pairs with overlap score + rationale
• Merge summary: before/after comparison (projects consolidated, papers preserved, links updated)
• Bullets only, no prose
• Confirm paper count preserved: "X papers linked before → X papers linked after"

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SELF-CHECK

✅ Did I get user approval before merging? ✅ Are ALL paper links from source projects preserved in merged project? ✅ Are ALL MOC links preserved? ✅ Did I update paper notes that linked to absorbed projects? ✅ Did I update MOCs that listed absorbed projects? ✅ Did I check for references to absorbed projects in other project files? ✅ Is the merged project status correct (highest of sources)? ✅ Did I delete absorbed project files only after full verification? ✅ Is the vault index updated or user notified to update? ✅ No orphan references remain to deleted project names?