Document availability of rsync for fetching deps in rebar.config.sample

It was previously possible to run `rebar compile deps_dir=/path/to/deps`,
but as of 70d27c5720331076f52e4fd7bcd1dc8045c8c86a, it was nixed.

This change fixes #310.

This allows an <app-name>.app.src.script to be defined and evaluated
when <app-name>.app.src or <app-name>.app are loaded. This allows the
user to add project specific manipulations to app metadata.

By default protobuffs doesn't create beams with debug info.  This
causes issues when running dialyzer which requires debug info.  Read
the `erl_opts` config and pass it down to protobuffs compiler.

The DirRef in the spec file is relative to the directory where the spec
file is located. ct2_rt was erroneously copying the spec file to test/.

eunit_test:function_wrapper/2 was renamed to eunit:mf_wrapper/2 in
R15B02. Ignore both calls like we do with escript:foldl/3.

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.

* re-compile rebar.erl instead of rebar_core to define VCS_INFO
* append "-dirty" if vcs indicates unclean repo status

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.