Duplicate rules cause directives and manually created rules to be discarded

[kalmakazi]

What version of gazelle are you using?

0.39.1

Does this issue reproduce with the latest releases of all the above?

Yes

What did you do?

Ran gazelle on a pkg containing a duplicate rule

What did you expect to see?

A successful run cleaning up the duplicate.

What did you see instead?

All directives and manually curated rules in the file are discarded and a corrupted graph is generated.

This is because when checkFile returns an error, the file is discarded:

bazel-gazelle/rule/rule.go

Line 142 in 99af6b3

func LoadData(path, pkg string, data []byte) (*File, error) {

And the only check checkFile performs is for duplicate rules:

bazel-gazelle/rule/rule.go

Line 1164 in 99af6b3

func checkFile(f *File) error {