Fix #267 (code path regression)

Since the introduction of -r/--recursive, deps were not properly added
to the code path when running ct, eunit, etc.

To fix that, pass a flag down to process_dir1 and conditionalize
execution of the command. This moves the decision into process_dir1
where we can choose to invoke preprocess/2 and postprocess/2 but not
execute the command.

Without this fix, you'd have to, for example, invoke 'rebar -r ct
skip_deps=true', if you wanted to run base_dir's ct suites with deps on
the code path (while skipping all non-base_dir ct suites).

So, with this patch applied, if you run
$ rebar ct
deps will be on the code path, and only base_dir's ct suites will be
tested.

If you want to test ct suites in base_dir and sub_dirs, you have to run
$ rebar -r ct skip_deps=true

If you want to test ct suites in all dirs, you have to run
$ rebar -r ct

The fix is not specific to ct and applies to all commands.