[bcomnes]

• Stacks on Update documentation paths on major bumps with ignore-next-line support #37; targets its branch so this PR contains only the follow-up cleanup.
• Fix tracked-file discovery in gitCommit to run from the repository root, allowing tracked files in ignored directories outside a nested WorkDir to be staged correctly. Add regression coverage for extra-only staging, bump-file staging, deduplication, and ignored untracked output.
• Assemble the automatically updated file list once for reporting and staging, and remove redundant CLI version-file injection while keeping ExtraFiles separate from update reporting.
• Extract rewriteDocumentationReference from the line scanner without changing reference matching or rewriting behavior.
• Cover documentation-enabled CLI dry runs and compare complete file lists so duplicate, unexpected, or incorrectly located paths fail tests.
• Verified with go test ./..., go test -race ./..., go vet ./..., go build ./..., and git diff --check. The staging regression failed before the fix and passes afterward.

[Copilot]

Copilot review overview

🟢 Approval recommended

The changes are focused, consistently tested, correctly formatted, and no unresolved issues were found.

Review effort: Balanced
Findings: None

What changed in this PR

Simplifies update-file plumbing and fixes staging of tracked ignored files outside nested work directories.

Changes:

• Discovers tracked files from the repository root.
• Separates automatically updated files from extra staged files.
• Expands regression coverage and extracts documentation-reference rewriting.

File	Description
version_skip_docs_test.go	Validates complete CLI file lists, including dry runs.
version_cli.go	Removes redundant version-file staging injection.
pkg/​goversion.go	Fixes staging discovery and consolidates changed-file assembly.
pkg/​git_commit_workdir_test.go	Covers nested-workdir staging and ignored files.
pkg/​documentation.go	Extracts single-reference rewriting logic.

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