Option to index git submodules as part of the parent project

Summary

Since 836c366 ("prune nested repositories from the parent source walk"), the source walker skips every non-root directory that contains a .git entry. That fixed a real problem (linked worktrees inside a checkout being indexed many times over), but it also drops git submodules from the parent project's index, with no setting to bring them back.

I'd like an opt-in way to index submodules as part of the parent, while still skipping linked worktrees and unrelated nested clones.

Use case

A "super repo" that pulls in the main application as a submodule:

super-repo/            <- where I start every agent session
  .gitmodules
  dev/                 <- scripts that launch and wrap the app
  docs/
  app/                 <- git submodule, ~1,000 tracked files

I always start agent sessions from super-repo/. Today:

The super-repo index covers only its own files; nothing under app/ is indexed, and nothing reports that it was skipped.
To search the app I have to tracedecay init it as a separate project and pass project_selector on every call, or use multi_root_* scope sets.
Even then there are no call or import edges between the two, so a path from dev/ into app/ never appears as one chain in callers / impact / call_chain.

For this layout the submodule is effectively part of the project, and one index is what I want.

Telling submodules apart from worktrees

With current git, both a linked worktree and a checked-out submodule have a .git file, not a directory, so the presence check can't distinguish them. Some signals that do:

The gitdir: target. A linked worktree points to <common-dir>/worktrees/<name>; a submodule points to <parent>/.git/modules/<name>.
The parent's index. A submodule is a gitlink entry (mode 160000) at that path, and is usually listed in .gitmodules.
Linked worktrees also show up in git worktree list for the parent.

Possible shape

Something like an index setting (name up to you):

[index]
include_submodules = true   # default false keeps today's behaviour

When enabled, the walker would descend into a directory only if it is a registered submodule of the root (gitlink plus .gitmodules entry), and keep pruning linked worktrees and other nested repositories exactly as now.

Environment

tracedecay 1.0.0-beta.91, macOS, Claude Code plugin install
git 2.54

fix(index): withdraw incomplete submodule source admission

Implementation investigation (2026-11-08 UTC), Refs #4593 — issue remains open; no fix is claimed.

A walker-only include_submodules switch cannot satisfy this issue without silently disagreeing with the indexed graph. I checked master at 91c72aba7750a398dd28e83d64bf0c6d6fef4172, root AGENTS.md (no nested AGENTS entries in the complete tree), the issue (zero comments before this investigation), both currently open PRs, and prior closed/unmerged #4719 (which explicitly withdrew a walker-only implementation).

The additional integration points that must change together are:

crates/tracedecay-code-index/src/source_walk.rs:167-176 excludes every nonroot .git directory; live grep, ast-grep, and unmounted-file auditing reuse this.
crates/tracedecay-code-index-runtime/src/code_index_scheduler/classification.rs builds candidates from the parent Git index and explicitly selects .index_worktree_submodules(None). The parent indexes the gitlink path, not the child source files.
crates/tracedecay-code-index-runtime/src/code_index_scheduler/git_tree_capture.rs explicitly skips entry.mode.is_commit(), so the clean-HEAD/exact-tree fast path drops gitlinks. reconcile.rs:4011+ uses that fast path to publish clean generations; merely changing the filesystem walker cannot affect the index.
freshness_witness.rs::source_candidates derives its roster from the parent classification, and identity.rs::GitMetadataFingerprintV1 samples only the parent Git metadata. A changed child revision or same-size content rewrite could otherwise remain falsely fresh.

An independent disposable native Git probe executed five nonvacuous assertions: the parent records 160000 ... app but not app/feature.rs; an initialized child has .git -> ../.git/modules/app; a linked worktree has a different .git -> .../worktrees/... target; and the child file really exists despite absence from the parent index. This is Git/filesystem behavior, not repository Rust/Bazel, CI, or native macOS validation.

Acceptance needs a single explicit, restart-applied opt-in from the canonical project configuration; Git-index gitlink plus .gitmodules membership and bound child repository/worktree identity; consistent nested-source admission, sanitized capture, sealed graph/retrieval, and both clean and dirty snapshot authorities; freshness invalidation on child changes and removals; fail-closed linked-worktree/untrusted clone/metadata substitution handling. Tests must exercise default-deny, opt-in parent→child call edges and grep/AST parity, commit/dirty change, restart/reuse, removal, denied/nested clone, and macOS/native behavior. No secondary walker-only authority.

No production changes or PR were published: the environment providing this investigation has no repository checkout or Bazel/native macOS toolchain, so it cannot legitimately compile, run nonzero repository tests, or establish a safe completed implementation. The issue-specific owner remains active; this comment is a concrete implementation boundary, not a closure recommendation.

fix(code-index): report skipped nested repositories in unmounted audit

fix(code-index): bound repository audits and report walk failures

style(code-index): format nested repository regressions

fix(code-index): align nested checkout capture with source walks

style(code-index): format nested repository boundary tests

fix(code-index): invalidate cached rosters on nested Git markers

test(code-index): assert roster invalidation across marker removal

fix(code-index): refuse markerless parent gitlink directories

style(code-index): satisfy Bazel formatting for gitlink guard

fix(code-index): deny ignored admission beneath Git gitlinks

fix(code-index): preserve HEAD gitlink boundary on staged removal

fix(code-index): deny staged-removal gitlink in source admission

style(code-index): fix ignored gitlink regression formatting

fix(code-index): preserve HEAD gitlink boundaries in classification

fix(code-index): preserve clean registered gitlink state

fix(code-index): deny gitlink children in freshness roster

fix(code-index): refuse symlinked source leaf capture

fix(code-index): reject failed submodule freshness witnesses

fix(code-index): preserve authenticated child capture on Windows

fix(code-index): revalidate lazy submodule source walks

fix(code-index): require explicit sealed submodule policy

perf(code-index): restrict scoped Git boundary traversal

style(code-index): apply Bazel rustfmt to scoped Git boundaries

fix(code-index): revalidate parent submodule authority during reads

style(code-index): apply Bazel rustfmt to submodule authority test

fix(code-index): recheck child repository worktree binding

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Option to index git submodules as part of the parent project #4593

Summary

Use case

Telling submodules apart from worktrees

Possible shape

Related

Environment

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Option to index git submodules as part of the parent project #4593

Description

Summary

Use case

Telling submodules apart from worktrees

Possible shape

Related

Environment

Activity

ScriptedAlchemy commented on Nov 8, 2026

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