Selective compilation with -s flag

[jlowin]

Summary

Add -s / --select flag to colin run to compile only the subgraph needed for specific files. The flag name allows future expansion to support glob patterns, tags, or subproject selectors.

Agent Context

Must read:

• Implement storage architecture: separate cache from published outputs #62 and ADR 018: docs/decisions/018-storage-architecture.md (storage separation enables this)
• Compile engine: src/colin/compiler/engine.py
• Dependency graph implementation

Blocked by: #62 (storage architecture must be implemented first)

Behavior

# Compile only file.md's subgraph, publish file.md + public deps
colin run -s file.md

# Multiple selections
colin run -s file1.md -s file2.md

# Don't clean output/ first (additive)
colin run -s file.md --no-clean

Default colin run (no -s)

1. Compile all files
2. Clean output/
3. Publish all public files

With -s file.md

1. Compute minimum subgraph to produce selected file
2. Compile subgraph (cache hits where possible)
3. Clean output/
4. Publish selected file + its public refs

Implementation

• Add -s / --select flag (repeatable)
• Add --no-clean flag
• Subgraph traversal: walk refs from selected file(s)
• Manifest: merge updates (don't touch entries outside subgraph)
• Cache in .colin/compiled/ preserved for files not in subgraph

Future expansion

The --select flag can grow to support richer selectors:

• --select "models/*.md" - glob patterns
• --select "tag:public" - tag filters
• --select "project:auth" - subproject filters

Use cases

• Large project, only need one output
• Faster iteration during development
• Minimize LLM calls when only one file changed

Related

• Implement storage architecture: separate cache from published outputs #62 - Storage architecture (enables this via .colin/ separation)

[jlowin]

also -- consider that users may only want to compile one file, not its upstreams (e.g. upstreams are fine, use their cache, but recompile this one). I'm not sure if we have that degree of precision now; --no-cache is going to reload all upstream files even with -s