Fix load order for custom project builders and parse transforms

The app data, when set by `rebar3_app_discover` basically does not
include the modules if it was derived from the .app.src file, even if at
a later point the modules were compiled.

Since there is currently no clear way to add that information reliably
across all compiler versions in all types of compilers, we simply clear
the cache and re-derive the information when required.

This might have a small performance cost, but is required for
correctness whenever an application's first build is run. Specifically,
this bug was detected when a plugin included lager's parse transform,
and the application itself also required it, but two distinct versions
were needed.

This patch finalizes fixing this issue.

Compile time with parse transforms needs to have the deps first in scope
before the plugins

Due to building dependencies with potential artifacts such as parse
transforms or macros, project builder plugins should be included in the
path, but _after_ deps are loaded.

Doing otherwise means that if any of the dependencies is required at
compile time, those of a plugin might get used first.

search subdirectories as well for imports/transforms/behaviours

Fix path coverage loading artifacts

Add hint for `rebar3 new help` on `rebar3 help new`

The old path handling routine would force loading a bunch of
applications, but it did not necessarily unload them aside from specific
calls that the other test handlers used to need to do, but no longer
needed under the updated path management of 3.7.0.

The leftover calls in the cover compilation bits caused some apps to be
loaded and to remain loaded before tests started.

fix base_compiler:run to take a single directory

fix to include beams built from src files in subdirs in modules list

Signed-off-by: Fred Hebert <mononcqc@ferd.ca>

Fix typespecs of new compiler behaviour

Updating manpages before 3.7.0

check last modified time on erl files for xrl and yrl files before compiling

Fix plugins list display to include project plugins

Support alias format {Namespace, Cmd} and {Namespace, Cmd, Args} (#1940)

add git clone --reference path support

fix install output result

templates/gitignore ignore emacs temp files

emacs creates temp files that ends with tilde (~).
These temp files should never be commited.
It is therefore safe to ignore them.

Signed-off-by: Niklas Johansson <raphexion@gmail.com>