If there are errors here, does it make sense to call ToPatches and SavePatchesToFile below?

yes, that was by design, although we may need to discuss about design choices here.

Btw, we need to write to empty string to nogoFixPath when there are errors. See nogo.go (line 100) for similar logic. Otherwise, bazel complains that the declared file is not defined.

Coming back to the design choices, here is another design in comparison:

if nogoFixPath != "" {
	// If nogo fixes are requested, save the fixes to the file even if they are empty.
	// This prevents Bazel from complaining about missing or invalid outputs.
	change, err := NewChangeFromDiagnostics(diagnostics, pkg.fset)
	if err != nil {
		// Ensure an empty patch file is saved when there's an error in generating the change.
		errs = append(errs, fmt.Errorf("error converting diagnostics to change: %v", err))
		if saveErr := SavePatchesToFile(nogoFixPath, nil); saveErr != nil {
			errs = append(errs, fmt.Errorf("error saving empty patches file: %v", saveErr))
		}
	} else {
		fileToPatch, err := ToPatches(Flatten(*change))
		if err != nil {
			errs = append(errs, fmt.Errorf("error generating patches: %v", err))
			if saveErr := SavePatchesToFile(nogoFixPath, nil); saveErr != nil {
				errs = append(errs, fmt.Errorf("error saving empty patches file: %v", saveErr))
			}
		} else {
			if err := SavePatchesToFile(nogoFixPath, fileToPatch); err != nil {
				errs = append(errs, fmt.Errorf("error saving patches to file: %v", err))
			}
		}
	}
}

In my current design, when NewChangeFromDiagnostics returns error, the change has partial result of fixes which can be still applied. Let us consider this case:
There are high-quality analyzers that produce great fixes, and there are some poorly written analyzers that produce wrong fixes, e.g., they produced corrupted offsets. Current design still allows the fixes from the well-written analyzers to be applied.

There is one caveat case: the change may already include some edits from the bad analyzer, which have valid offsets but are of poor quality.

In my opinion, the nogo framework should faithfully apply the fixes that are applicable (i.e., those with valid offsets). It should not ban fixes from all analyzers in the case that one analyzer is bad. Also it is the responsibility of the monorepo owners to remove/fix bad analyzers.

Let me know your thoughts,

if we adopt my current design, I also updated NewChangeFromDiagnostics to more permissive.

I like the ability to let user choose analyzers to trust

can we return bytes instead? The out is converted to string here and immediately converted back to []byte by its only caller

Do we need 3 levels of nesting, only to be flattened later?

yes, we need this.

the two levels file:edits is required, since we track and apply patch per file.

besides, see the Flatten() function, it considers the cases that different analyzers produce conflicting edits, i.e., edits that overlap with each other. In this case, it is impossible to apply both edits.

we will ignore the latter analyzer (sorted already for determinism) but still allow the former analyzer to proceed.
This is why we add the extra indirection of indexing by analyzer.

Let's avoid overusing maps and create more informative data structure: https://abhinav.github.io/future-proof-packages-2023/#/%EF%B8%8F-map-overuse

this is the same, right?

Test utilities should be in _test.go. Putting here and export it means it's part of public API

if difflib.SplitLines doesn't work well, can we not use it? It's also inefficient: you first read the whole file into the memory and then split it, which doubles the memory usage. You could just read the file line by line with bufio.Scanner

I like the ability to let user choose analyzers to trust

Can we produce one patch file per analyzer? That way, we don't need to merge edits to the same file from different analyzers. Like you said, some analyzers may produce bad edits. When users apply patches one by one, they can ignore those patched produced by bad analyzers.