feat(cli): Add `papi attach` command for upgrading paper assets

[hummat]

Problem or Motivation

Users cannot fix missing or low-quality assets after initial paper ingest. Common scenarios:

• Downloaded PDF is corrupted or scan-only → need to attach better PDF
• arXiv paper had no LaTeX source → want to attach .tex files later
• Want to regenerate summaries/equations after attaching new source

Proposed Solution

Add papi attach command:

papi attach PAPER --pdf /path/to/better.pdf
papi attach PAPER --source /path/to/main.tex
papi attach PAPER --pdf new.pdf --regen auto

Options

• --pdf PATH: Replace PDF file
• --source PATH: Add/replace LaTeX source (file or directory)
• --regen {auto,equations,summary,tags,tldr,all}: Regenerate artifacts after attachment
  • auto: regenerate only what the new attachment enables (e.g., equations from LaTeX)
  • Specific: regenerate only specified artifact
  • all: regenerate everything
• --backup: Create backup before replacement (default: true)

Implementation

Complexity: LOW — straightforward file operations + meta.json updates

1. Validate paper exists in index
2. Backup existing files if --backup (default)
3. Copy new files to ~/.paperpipe/papers/{name}/
4. Update meta.json with new file paths/metadata
5. Run regeneration if --regen specified
6. Update index

Alternatives Considered

• Re-run papi add with new files — would require delete + re-add, losing metadata
• Manual file replacement — error-prone, doesn't update meta.json

Area

CLI commands