Github user dpogue commented on the issue:
https://github.com/apache/cordova-android/pull/321
With regards to point 1 above, I've found the root cause:
In a project-level config.xml, `resource-file` is only supported under a
`platform` tag. These files get copied into the native platforms.
Within each native platform, there's a config.xml specific to that
platform. When the `resouce-file` tags are copied into this file, they are not
nested under a `platform` tag. This means `ConfigParser.getFileResources` was
not finding them, and hence returning an empty list of files to clean.
I've opened https://github.com/apache/cordova-lib/pull/547 to add an option
to `ConfigParser.getFileResources` to return the top-level `resource-file` tags.
I've also opened https://github.com/apache/cordova-ios/pull/309 (iOS) and
https://github.com/apache/cordova-android/pull/377 (Android) to pass in that
new option when cleaning.
I will look into getting unit tests for Android's prepare step set up to
address the rest of the feedback.
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