clean and _checkouts results in repeated actions

[talentdeficit]

this is using the app structure setup by the build_checkouts_dep test in the compiler test suite

$ ~/dev/rebar3/rebar3 version
rebar 3.0.0-beta.3+build.3089.ref97ae8d6 on Erlang/OTP 18 Erts 7.1
$ cat rebar.config
{deps,[{checkapp2_635554,"69.11.8",{git,[],[]}}]}.
$ ~/dev/rebar3/rebar3 compile
===> Verifying dependencies...
===> Compiling checkapp2_635554
===> Compiling checkapp1_818211
$ ~/dev/rebar3/rebar3 clean
===> Cleaning out checkapp1_818211...
$ ~/dev/rebar3/rebar3 clean --all
===> Cleaning out checkapp1_818211...
===> Cleaning out checkapp2_635554...
===> Cleaning out checkapp1_818211...

[tsloughter]

This isn't related to checkouts.

$ rebar3 clean -a
===> Cleaning out bbmustache...
===> Cleaning out certifi...
===> Cleaning out cf...
===> Cleaning out erlware_commons...
===> Cleaning out getopt...
===> Cleaning out providers...
===> Cleaning out rebar...
===> Cleaning out relx...
===> Cleaning out ssl_verify_hostname...
===> Cleaning out rebar...

See, it cleans out rebar twice. It is because all finds all apps in _build/<profile>/lib which will include the project app and then cleans out the project apps.

Should be easy to fix, not decided what the best solution is yet.

[tsloughter]

Fix #890