Deprecate old plugin target-dir structure support

Old plugin target-dir structure support, which needs special remapping code in `bin/templates/cordova/lib/pluginHandlers.js` and has led to so many issues, should be deprecated with a warning message for future removal.

Plugin authors should be able to specify exactly where source files should be installed. `lib-file` elements should be used for JAR, AAR, etc. Use of `lib-file` elements for Android NDK `.so` files should be properly supported (#557).

Start in bin/templates/cordova/lib/pluginHandlers.js and read the special remapping code for the old plugin target-dir structure. Review issue #557 for the related lib-file handling requirements; done means old target-dir usage produces a deprecation warning and the stated lib-file cases are properly supported.

Written by the indexing model from the issue text.