1. manually insert directory entries to work around issues fixed in
   R15B02 erl_prim_loader
2. put the escript archive's beams in appname/appname/ebin

Tested with R13B03 and R15B01.

Use erl_prim_loader:read_file_info instead of filelib:is_file to make
sure paths inside the escript archive are handled properly.

When rebar ct executes with its default common test directory of "test",
it will generate a hardcoded "logs" directory in every application with
a test directory present, causing an overlap with eunit's test framework
so even test directories with only eunit tests will be processed by ct.

reltool is missing an app resource file before R14A.
Therefore, restore the old check and add TODO.