This commit adds new checks in the `set_paths` test case related to
runtime apps and their path handling with the `runtime` target in
`rebar_paths`. These new checks also hope to increase the coverage
of the changes done to the xref provider in this same PR (#2354).

This commit also adds some new helper functions to help deal with
future changes related to these new checks (i.e., changes related to
the runtime apps), besides fixing a problem when looking for the
first instace of an app/dep/plugin in the path while testing.

- Only set paths that need to be put as a priority
- Clean up paths before leaving API mode

The first point accounted for some performance cost, but the latter one
explains the 40% overhead in test runs: since rebar3 calls rebar3 a lot
with a bunch of fake apps, and that the new mechanism for path handling
by default does not _remove_ paths, it just _orders_ them, we would end
up in a situation where as the tests ran, more and more fake paths would
get added to the VM.

By the time the run was over, all path handling would take longer since
more paths needed filtering every time. By resetting paths at the end of
an API run, we prevent a given 'project' from polluting another one's
runtime and performance once the API successfully returns.

Some finishing touch to that code

Move path management out of rebar_utils manual code path function
handling (which we leave there for backwards compat), and centralize
them to allow easier coordination of paths between plugins and deps.

On top of path handling, do a check of loaded modules to only purge and
reload those that actually need it done in order to prevent all kinds of
weird interaction and accidental purge kills. It also allows the
possible cohabitation of both at once, with a "in case of conflict pick
X" as a policy

Changing path handling in providers also highlighted a bunch of bugs in
some tests and appears to fix some in other providers, specifically
around plugins.