bug: apply fail to apply to correct files - create a new file instaed

[olejorgenb]

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Bug Description

My project have this structure:

scripts/
src/
src/scripts/

When I work with files inside src/scripts/ apply create a new file in scripts/ instead of modifying the file inside `src/scripts/. This happens even when I only include the single file as context.

Additional context

No response

[linear]

BUGS-797 bug: apply fail to apply to correct files - create a new file instaed