Organize src/core into real modules

[benvinegar]

Problem

src/core had become a pile of ~30 loose files that any code anywhere could reach into. The worst symptom was core/types.ts: 147 files imported it, it mixed four unrelated audiences (the changeset model, CLI inputs, app bootstrap, and re-exported extension contract types), and touching it invalidated a big chunk of the typecheck graph. There was no way to tell which files were "API" and which were internals — everything was public because nothing said otherwise.

flowchart TD
  ui["src/ui"] --> types
  app["src/app"] --> types
  session["src/session"] --> types
  ext["src/extensions"] --> types
  types["core/types.ts — 147 importing files<br/>changeset model + CLI inputs + bootstrap<br/>+ re-exported extension contract types"]
  types -.->|re-exports for| loose["~30 loose files at core/*<br/>config, loaders, terminal, pager, paths, errors, …<br/>all public, nothing says otherwise"]
  loose -.->|some import back| types

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What this does

Core is now a set of directories named for what they hold, each with a declared public surface, and core/types.ts is gone — every file imports the module that actually declares the thing it wants, so the dependency graph shows real relationships instead of "everything depends on types.ts".

flowchart TD
  ui["src/ui"] --> changeset
  ui --> run
  ui --> process
  app["src/app"] --> bootstrap
  app --> changeset
  app --> run
  session["src/session"] --> changeset
  session --> run
  subgraph core["src/core"]
    bootstrap["bootstrap.ts<br/>AppBootstrap + ReloadContext<br/>28 importers, down from 147"]
    changeset["changeset/<br/>the model + how it loads<br/><i>internal: fromPatch, sidecar,<br/>fileLanguageLookup</i>"]
    run["run/<br/>what a run was asked to be:<br/>inputs, config, command catalog"]
    process["process/<br/>where it executes: terminal,<br/>pager, job control, shutdown"]
    existing["review/ vcs/ theme/<br/>watch/ patch/<br/><i>already coherent, unchanged</i>"]
  end
  bootstrap --> changeset
  bootstrap --> run

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The module boundaries aren't just convention: a dependency-cruiser rule fails CI if anything outside a module imports its internals, and a reachability rule fails on any src/ file no entry point can reach — which is how core/review/address.ts (zero consumers) got deleted.

Reviewing this

It's a big diff but a shallow one: everything is git mv plus import-path updates. No exported symbol was renamed and no behavior changed — the published hunkdiff/extension and hunkdiff/opentui entry points are untouched. The commits are reviewable independently if the whole thing is too much at once.

Three judgment calls worth an opinion:

• core/review/annotations.ts turned out to genuinely use AgentAnnotation from extension-api/types — the old shell was hiding that edge. The seam test now allows that single file as a containment target rather than pretending the dependency doesn't exist.
• changeset/loaders.ts imports the bootstrap type it assembles (loadAppBootstrap), which is backwards for the layering. It's a named exception in the rules; moving that function up to src/app would retire it, left as a follow-up.
• AgentCard.tsx + agentPopover.ts appear to be dead (nothing renders them since notes moved into the diff flow) but only their tests keep them alive. They're quarantined in the dead-module allowlist instead of deleted — happy to delete them here if you agree they're gone.

🤖 Generated with Claude Code

https://claude.ai/code/session_01XcuayyxJrwQd9EHpuxNef1

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1 Skipped Deployment

Project	Deployment	Actions	Updated (UTC)
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[benvinegar]

@greptile-apps review

[greptile-apps]

Greptile Summary

This PR reorganizes the loose src/core files into changeset, run, and process modules, retargets consumers to the declaring modules, and adds dependency rules that enforce module interiors and production reachability.

• Splits the former core/types.ts surface among bootstrap and domain-owned modules.
• Moves changeset acquisition, run configuration, and process-lifecycle files into coherent directories.
• Adds dependency-cruiser checks for dead modules and prohibited interior imports.
• Deletes an unused review-address implementation and documents the resulting boundaries.

Confidence Score: 4/5

The PR appears safe to merge, with only non-blocking stale module names in the architecture documentation.

The declaration split, import rewrites, published entrypoints, and type-only bootstrap dependency remain coherent; the accepted issue is limited to documentation that still references superseded directory names.

Files Needing Attention: docs/module-boundaries.md

Important Files Changed

Filename	Overview
.dependency-cruiser.cjs	Adds production-reachability and core-interior dependency constraints with explicit entrypoint and test-only allowlists.
src/core/bootstrap.ts	Retains the launch-composition types formerly declared by the broad core types module.
src/core/run/commandInputs.ts	Consolidates CLI and session command input contracts without an identified behavioral change.
src/core/changeset/loaders.ts	Relocates changeset loading and retains only a type-level dependency on the bootstrap contract.
docs/module-boundaries.md	Documents the new architecture comprehensively but retains several stale invocation/runtime directory names.
docs/source-architecture.md	Updates the ownership map to include changeset, run, and process modules.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
  App[src/app] --> Bootstrap[src/core/bootstrap.ts]
  App --> Changeset[src/core/changeset]
  App --> Run[src/core/run]
  App --> Process[src/core/process]
  Bootstrap --> Changeset
  Bootstrap --> Run
  Bootstrap --> Process
  UI[src/ui] --> Changeset
  UI --> Run
  UI --> Process
  Rules[dependency-cruiser rules] -. enforce interiors .-> Changeset
  Rules -. enforce reachability .-> App

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Prompt To Fix All With AI

### Issue 1
docs/module-boundaries.md:168-169
**Stale core module names**

The final bootstrap dependency list still names `invocation` and `runtime`, although this PR establishes `run` and `process`; these stale paths direct maintainers toward nonexistent module names, and the same terminology remains in the final module inventory below.

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (1): Last reviewed commit: "fix(bench): repoint highlight-cache-laye..." | Re-trigger Greptile}

[greptile-apps]

Stale core module names

The final bootstrap dependency list still names invocation and runtime, although this PR establishes run and process; these stale paths direct maintainers toward nonexistent module names, and the same terminology remains in the final module inventory below.

Prompt To Fix With AI

This is a comment left during a code review.
Path: docs/module-boundaries.md
Line: 168-169

Comment:
**Stale core module names**

The final bootstrap dependency list still names `invocation` and `runtime`, although this PR establishes `run` and `process`; these stale paths direct maintainers toward nonexistent module names, and the same terminology remains in the final module inventory below.

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.