fix: preserve trailing newlines in text-based 3-way merges

[Jorrit Elfferich (jorrite)]

what

• Fix atmos scaffold generate --update unconditionally stripping the trailing newline from every file it 3-way-merges, whether or not the file actually changed.
• pkg/generator/merge/text_merger.go: TextMerger.Merge() now appends one newlineSeparator ("\n") to each of ours/base/theirs before handing them to diff3.Merge, so diff3's guaranteed loss of exactly one trailing newline cancels out and the original count survives.
• pkg/generator/merge/text_merger_test.go: consolidated the trailing-newline regression coverage into a single table-driven test, TestTextMerger_TrailingNewlinePreservation, asserting exact byte-for-byte output across a no-op merge (0/1/2/3 trailing newlines, plus an internal blank line) and a genuine template change (theirs with 0/1/2 trailing newlines).
• No change to conflict detection, threshold behavior, or ConflictStrategy handling — out of scope, and unaffected since the appended newline is identical across all three inputs.

why

• TextMerger.Merge() delegates the actual 3-way merge to epiclabs-io/diff3, which reads each of base/ours/theirs line-by-line via bufio.Scanner (ScanLines, Go's standard-library default split function) and rejoins the merged lines with strings.Join(lines, "\n").
• ScanLines strips every line's terminator — including the last — and gives no way to tell afterward whether the original input ended with a trailing newline or not. Concretely: for content ending in N trailing newlines, the round-trip through GetLines + Join always reconstructs exactly N-1 (it loses exactly one, regardless of how many there were; for N = 0 there was nothing to lose in the first place). Verified directly: generating a file with 3 trailing newlines and running --update with nothing changed on the template side reproducibly comes back with 2.
• Appending one newline to each input before the merge bumps every input's count to at least 1, so that guaranteed loss of exactly one cancels out and the original count is preserved — for both the no-op case and genuine changes, since whichever side's content ends up dominating a given region carries its own (now-restored) newline count through, independent of the others.
• This must be applied to all three inputs, not just theirs: appending it only to theirs makes an otherwise-identical ours/theirs pair (a very common no-op shape) differ by one trailing newline as far as diff3 is concerned, which turns a no-op into a spurious detected change/conflict instead of fixing anything.

references

• Closes scaffold generate --update strips trailing newlines (if any) from every merged file #2887.

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• docs/fixes/2026-08-10-scaffold-update-trailing-newline.md

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• docs/fixes/2026-08-10-scaffold-update-trailing-newline.md

---

📝 Walkthrough

Walkthrough

TextMerger.Merge now preserves trailing-newline counts by appending a newline to each diff3 input. Tests verify byte-exact output for unchanged and template-only merges. Documentation records the fix.

Changes

Trailing-newline preservation

Layer / File(s)	Summary
Text merge and validation pkg/generator/merge/text_merger.go, pkg/generator/merge/text_merger_test.go, docs/fixes/...	TextMerger.Merge appends a newline to each diff3 input. Tests cover trailing-newline and blank-line states. Documentation describes the updated merge behavior and validation.

Estimated code review effort: 2 (Simple) | ~10 minutes

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the main change: preserving trailing newlines in text-based 3-way merges.
Linked Issues check	✅ Passed	The implementation and regression tests address issue #2887 by preserving trailing newlines for unchanged and updated text merges.
Out of Scope Changes check	✅ Passed	The implementation, tests, and fix documentation directly support issue #2887 and introduce no unrelated changes.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
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Inline comments:
In `@pkg/generator/merge/text_merger_test.go`:
- Around line 820-839: Extend the merge test cases around the existing
genuine-change scenarios to cover template-only EOF newline changes: keep base
and ours identical, and verify theirs both adds and removes trailing newlines,
including “line 1\n” to “line 1\n\n” and “line 1”. Set each expected result to
preserve theirs’ newline count.
- Around line 756-761: Add a Go doc comment beginning with “Merge” immediately
before the exported TextMerger.Merge method, documenting its purpose and the
newline behavior referenced by TestTextMerger_TrailingNewlinePreservation. Keep
the existing test comment unchanged.

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• pkg/generator/merge/text_merger.go
• pkg/generator/merge/text_merger_test.go

[Erik Osterman (Cloud Posse) (osterman)]

Please run the /fix-log to the update fix log (claude skill).

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.82%. Comparing base (21c5899) to head (cb66a31).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2891      +/-   ##
==========================================
- Coverage   82.83%   82.82%   -0.02%     
==========================================
  Files        1866     1866              
  Lines      181277   181277              
==========================================
- Hits       150160   150135      -25     
- Misses      23313    23329      +16     
- Partials     7804     7813       +9     

Flag	Coverage Δ
unittests	82.82% <100.00%> (-0.02%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
pkg/generator/merge/text_merger.go	89.38% <100.00%> (ø)

... and 12 files with indirect coverage changes

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These changes were released in v1.226.0-rc.5.