Fix problems in CI failures (travis and semaphore)

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.