Improve test coverage: 37 new command contract tests + fix nuke-without-kill re-init

[Copilot]

Coverage was ~53%. Adds 37 integration tests targeting the highest-value gaps — command output contracts, config accuracy, and complex workflows — and fixes three real bugs uncovered in the process.

New tests (tests/command_contract_tests.rs)

• Shell completions — completeme for bash/zsh/fish/nushell; asserts non-empty output and subcommand name presence
• add --no-init — config-only add without cloning; subsequent init materializes it
• nuke-it-from-orbit — --all clears every submodule; reinit (without --kill) restores the clone and preserves sparse-checkout patterns
• generate-config — --from-setup reads .gitmodules; --force overwrites existing file (no-force fails)
• change — path relocation (delete+re-clone), URL swap, active toggle, sparse-path replace vs. append, multiple fields in one call
• change-global — persists update/fetch fields; errors without args
• Error contracts — nonexistent targets for delete, disable, change, nuke all fail with an informative message
• Output phrase contracts — exact strings asserted for every command (add, check, init, reset, sync, update, list, disable, delete)
• Config persistence — all fields written by add; multiple adds all survive; delete preserves sibling sections

Bug fixes (discovered by the new tests)

nuke-without-kill fails to re-initialize — three-layer bug

1. --branch . is invalid for git submodule add

"." is the .gitmodules encoding for CurrentInSuperproject; passing it as a --branch argument causes fatal: 'HEAD' is not a valid branch name. The CLI fallback now skips the flag when the branch resolves to ".".

2. git2 uses path as key, cleanup used name

git2::Repository::submodule() keys .git/config and .git/modules/ by path (e.g. lib/reinit), not by name (e.g. reinit-lib). After a delete, the name-based cleanup left stale path-based artifacts that caused git2's subsequent add to fail. delete_submodule_by_name and the CLI fallback now remove both.

# Before fix: stale after delete
.git/config         → [submodule "lib/reinit"]   ← not cleaned
.git/modules/       → lib/reinit/                ← not cleaned

# After fix: both key forms removed

3. git2 Repository object caches stale submodule state

Even after filesystem cleanup, the in-memory git2::Repository still believed the submodule existed and refused to re-add it. delete_submodule_by_name now calls git_ops.reopen() — a new method on GitOpsManager — to reopen the repository from disk after a destructive operation.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• invalid-host
  • Triggering command: /usr/bin/ssh /usr/bin/ssh -o SendEnv=GIT_PROTOCOL git@invalid-host git-upload-pack 'user/repo.git' user.email test@example.com git /usr/libexec/gccgit low /home/REDACTED/.ru-m git clea�� low /home/REDACTED/.ruInitial commit k/_temp/ghcca-node/node/bin/git gnu -plugin /usr/local/sbin/user.email git (dns block)
  • Triggering command: /home/REDACTED/work/submod/submod/target/debug/submod /home/REDACTED/work/submod/submod/target/debug/submod add git@invalid-host:user/repo.git --name invalid-test --path lib/invalid p/bin/git README.md basename nfig/composer/ve--revs git init�� /tmp/.tmpv1ER8k/--delta-base-offset it git HEAD refs/heads/main /home/REDACTED/wors/-/ / git (dns block)
  • Triggering command: /usr/bin/ssh /usr/bin/ssh -o SendEnv=GIT_PROTOCOL git@invalid-host git-upload-pack 'user/repo.git' -fdx (dns block)
• nonexistent.domain.invalid
  • Triggering command: /home/REDACTED/work/submod/submod/target/debug/submod /home/REDACTED/work/submod/submod/target/debug/submod add REDACTED --name invalid-test --path lib/invalid /usr/lib/git-core/git s/rustcRJ12FY/sygit s/error_handlingconfig s/error_handlinguser.email git rev-�� --git-dir s/error_handling_tests-1388c0cc70dcfabb.43s2t6zslib/large k/_temp/ghcca-node/node/bin/git s/error_handlinggit s/error_handlingrm s/error_handling--cached git (dns block)
  • Triggering command: /usr/lib/git-core/git-remote-http /usr/lib/git-core/git-remote-http origin REDACTED git conf�� user.email test@example.com nfig/composer/vendor/bin/git (dns block)
  • Triggering command: /home/REDACTED/work/submod/submod/target/debug/submod /home/REDACTED/work/submod/submod/target/debug/submod add REDACTED --name invalid-test --path lib/invalid /home/REDACTED/work/_temp/ghcca-node/node/bin/git user.email test@example.comconfig /usr/local/.ghcuuser.email git conf�� user.name Test User /home/REDACTED/.dotnet/tools/git user.email test@example.comconfig nfig/composer/ve--remove-section git (dns block)
• nonexistent.invalid.domain.test
  • Triggering command: /home/REDACTED/work/submod/submod/target/debug/submod /home/REDACTED/work/submod/submod/target/debug/submod add REDACTED --name timeout-test --path lib/timeout k/_temp/ghcca-node/node/bin/git (dns block)
  • Triggering command: /usr/lib/git-core/git-remote-http /usr/lib/git-core/git-remote-http origin REDACTED git conf�� protocol.file.allow always /usr/local/.ghcup/bin/git target/debug/depgit target/debug/deprm target/debug/dep--cached git conf�� user.email test@example.com k/submod/submod/target/debug/submod target/debug/depgit target/debug/depsubmodule cal/bin/cc k/submod/submod/--name (dns block)
  • Triggering command: /home/REDACTED/work/submod/submod/target/debug/submod /home/REDACTED/work/submod/submod/target/debug/submod add REDACTED --name timeout-test --path lib/timeout it origin main p/bin/git git init�� e /home/REDACTED/work/submod/submod/--all rgo/bin/git --all --kill ndor/bin/git git (dns block)

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[codecov]

Codecov Report

❌ Patch coverage is 81.53846% with 12 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/git_ops/mod.rs	82.05%	7 Missing ⚠️
src/git_manager.rs	80.76%	5 Missing ⚠️

Files with missing lines	Coverage Δ
src/git_manager.rs	88.91% <80.76%> (+15.37%)	⬆️
src/git_ops/mod.rs	75.73% <82.05%> (+1.10%)	⬆️

... and 5 files with indirect coverage changes

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• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

This PR expands integration coverage around the submod CLI’s command/output contracts and fixes a re-init failure in the nuke-it-from-orbit (without --kill) workflow by improving submodule cleanup and refreshing git2 repository state.

Changes:

• Add a large new integration test suite validating command output phrases, error contracts, config persistence, and multi-step workflows.
• Fix submodule re-init after delete/nuke by cleaning both name-based and path-based git artifacts and reopening the git2 repository state.
• Adjust git CLI fallback to avoid passing an invalid --branch . to git submodule add.

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 2 comments.

File	Description
tests/command_contract_tests.rs	Adds extensive integration tests covering command behavior, output contracts, and config accuracy/persistence.
src/git_ops/mod.rs	Adds workdir()/reopen(), improves cleanup of path-keyed submodule artifacts, and skips invalid --branch . in CLI fallback.
src/git_manager.rs	Strengthens delete cleanup for path-keyed artifacts and calls git_ops.reopen() post-delete to avoid git2 cached state issues.
Cargo.lock	Removes an unused dependency entry (serde_json).

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[bashandbone]

Really strong work on this PR; identifying important bugs and filling testing gaps.

[bashandbone]

@copilot The build is failing in CI with linting errors:

error[E0308]: mismatched types
    --> src/git_manager.rs:1341:16
     |
1341 |         if let Err(e) = self.git_ops.reopen() {
     |                ^^^^^^   --------------------- this expression has type `()`
     |                |
     |                expected `()`, found `Result<_, _>`
     |
     = note: expected unit type `()`
                     found enum `Result<_, _>`

For more information about this error, try `rustc --explain E0308`.

Please run clippy/rustfmt and make sure to resolve all errors and warnings.

[Copilot]

@copilot The build is failing in CI with linting errors:

...

Fixed in 4123e53. reopen() now returns Result<()> — it returns an error if the git2 backend (required) fails to reopen, while gix failures (optional backend) are logged as warnings and treated as non-fatal. This both fixes the type mismatch and addresses the reviewer's concern about silent error masking.