Remove inner metadata index.json (metadata/<groupId>/<artifactId>/<version>/index.json) from the repository (Part #1)

[jormundur00]

What does this PR do?

In this PR we remove the unnecessary inner, version-based, metadata index.json file. This file was only used to verify the contents of the specific version directory (to verify that all files listed in the index.json are present in the directory, and no additional files are present). This file seems redundant, as the MetadataFilesCheckerTask already checks if all the files listed in the inner directory are specific metadata files (so checking if the files match the files listed in index.json seems unnecessary).

The removal of this file is important for the 1.0.0 release of GraalVM Reachability metadata, as we aim to simplify the addition of new metadata to the repository, as well as remove the extra overhead we got from the additional JSON files.

As this PR aims to modify all existing metadata directories, it has to be split into two PRs to avoid reaching the GitHub Actions job limit.

Fixes: #846

[jormundur00]

The "Test changed metadata" and "Test changed build logic" checks fail here because we try to remove the index.json file located in metadata/org.eclipse.angus/jakarta.mail/1.0.0, but the global index.json (located in metadata/index.json) has no entry for that artifact.

Looking at the PR where metadata for this artifact was added it was, probably by mistake, not added to the global index.json, and the metadata for it was not changed since, so this check never ran.

I can add it to the index.json in this PR (or we can open a separate issue for it), but I'm unsure which allowed-packages should be listed for this artifact.

CC: @vjovanov @kimeta

[vjovanov]

The redness of this PR expresses the usefulness of this feature.

[kimeta]

The "Test changed metadata" and "Test changed build logic" checks fail here because we try to remove the index.json file located in metadata/org.eclipse.angus/jakarta.mail/1.0.0, but the global index.json (located in metadata/index.json) has no entry for that artifact.

Looking at the PR where metadata for this artifact was added it was, probably by mistake, not added to the global index.json, and the metadata for it was not changed since, so this check never ran.

I can add it to the index.json in this PR (or we can open a separate issue for it), but I'm unsure which allowed-packages should be listed for this artifact.

CC: @vjovanov @kimeta

This seems to me like a bug as well. allowed-packages should cover the packages of the classes specified in the condition entries within the config files. In this case "jakarta" should work.
Also checkMetadataFiles will probably fail due to missing condition entries in the metadata/org.eclipse.angus/jakarta.mail/1.0.0/resource-config.json.