[TIMOB-15198] [TIMOB-14884] iOS bugs and support files for Android build

[TIMOB-15198] Fixed bug with plugins not being loaded correctly and thus Alloy not being triggered.

[TIMOB-14884] Fixed bug in iOS build with the platform specific folders not being copied over top the root level files.

Also included a handful of Android build related changes that should not affect the old python-based Android build.