Cover gets slower and slower for each application. This is due to the
cover_server internal state. Stopping the cover server between
eunit+cover runs, emptying the cover_server state, gives a ~5-6x speed
improvement when analyzing many Erlang modules. Stopping the cover
server replaces the earlier practice of doing a cover:reset before each
run. On a project consisting of 62 dependencies with a total of 1866
Erlang modules the running time of rebar eunit decreased from ~20
minutes to ~3 minutes.

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.