Fix more qmk generate-api fallout from userspace support

[sigprof]

Description

After #22222 list_keymaps(fullpath=True) returns absolute paths which might point to the userspace directory tree; however, the implementation of qmk generate-api expected to get paths relative to qmk_firmware. The problem was partially fixed in #22618 for the generated url value; however, the path value for keymaps was still incorrect (this also made the subsequent code overwrite the keymap.json files in the working copy instead of writing those files converted to plain JSON into the API output directory).

Fix the path value for keymaps to contain the keymap path relative to qmk_firmware as it was before the userspace changes, and skip any userspace keymaps which might have been found.

Types of Changes

• Core
• Bugfix
• New feature
• Enhancement/optimization
• Keyboard (addition or update)
• Keymap/layout/userspace (addition or update)
• Documentation

Issues Fixed or Closed by This PR

• The generated API files for keyboards had broken path values for JSON keymaps (instead of paths relative to the qmk_firmware directory, which were also suitable to retrieve the keymap.json files from the API, these values contained absolute paths from the machine where the API files were generated).
• The generated API files did not contain any keymap.json files (the generate-api code was writing those files over the original keymap.json files in the working copy instead of placing them under the API output directory).
• Running qmk generate-api while also having user.overlay_dir configured could fail if the userspace overlay contained any JSON keymaps.

Checklist

• My code follows the code style of this project: C, Python
• I have read the PR Checklist document and have made the appropriate changes.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• I have tested the changes and verified that they work and don't break anything (as well as I can manage).