Fix problems in CI failures (travis and semaphore)

In the Makefile.am, switched out the fetch (which can have auth problems
in certain envs) with a simple branch per @perlpunk++'s suggestion.

With the new test branches, travis had a problem in that it only clones
one branch and we need the other branch refs to be available. Fixed this
by fetching the other branch refs. I also cleaned up the travis YAML
file.

The Ubuntu 14.04 docker image (used by semaphoreci) had an older git,
without the worktree command, so I made it install the latest git from a
ppa.

Renamed tests/run-tests.sh to tests/run-all-tests.sh for tab completion
conflict reasons.