Submodule diffs and pull requests for umbrella projects

[NeilMazumdar]

Setup

I run T3 Code on an umbrella repository with 70 direct submodules in four grouping folders. The umbrella holds docs, configuration and submodule pins. All implementation work happens inside the submodules. The agent edits files in a submodule, commits there, and opens a pull request on that submodule's repository.

Splitting this into 70 projects would give up the reason the umbrella exists. One thread often changes an API repo and the frontend that calls it, and the agent needs both in view.

What happens today

Checked against main at 07cb9028.

Diffs. An uncommitted edit inside a submodule never reaches the thread's Changed files or Diff panel. The working-tree diff reports 0 0 lib and Subproject commit <sha>-dirty. After a commit inside the submodule, the diff shows only the gitlink change (mode 160000) with no file-level diff. No diff call passes --submodule=diff, and checkpoint capture (add -A into the checkpoint index, then write-tree) records only the gitlink.

Pull requests. The Pull requests page searches one repository per project, built from each project's remote (repo:owner/name in PullRequestService.ts). A pull request the agent opened on a submodule's repository never appears there, even when it came from a thread in the umbrella project.

Request

1. Show changes inside initialized submodules in Changed files, Diff and the per-turn checkpoint view, grouped by submodule. This is the ask in Feature request: show submodule changes in git diff view #6688. I'm raising it again here because the pull request list needs the same submodule discovery.
2. Include pull requests from the repositories of a project's initialized submodules on the Pull requests page, with a filter by submodule, and let the review view open them.

An opt-in per project, such as a t3.json field, would be fine. Walking 70 submodules on every status refresh has a real cost.

Workaround

Adding each submodule folder as its own project should give per-repository diffs and pull requests. It loses the single thread that spans repositories, and means 70 projects in the sidebar.

Related: #6688, #20282 (closed as a duplicate of #6688).