[recipes:update] Keep files modified in the app when the recipe removes them

[lyrixx]

Q	A
Bug fix?	yes
New feature?	no
Deprecations?	no
Issues	Fix #1105
License	MIT

When a new version of a recipe no longer ships a file, recipes:update ran git rm on it even if it had been modified in the app, then reported "No files were changed as a result of the update."

Now, RecipePatcher::generatePatch() compares the file in the app with the one copied by the original recipe:

• same content: the file is deleted, as before;

• different content: the file is kept, and listed in a warning, like the files still referenced by other recipes:

  The following files were removed in the recipe, but they were kept because you modified them. You might need to remove them manually:
        - config/packages/workflow.yaml
  

Deleted files are now also taken into account to decide whether files were changed by the update.

Reporting this as a modify/delete conflict is not possible with git apply, which is why deletions were moved out of the patch in the first place.

I also fixed two tests: testGeneratePatch created the app files with touch (empty, so now seen as modified), and testIntegration checked the deletion of security.yaml at the wrong path, so the assertion always passed.