Show path to executable if version-checking fails to identify version.
Improve documentation, add a few sanity-checks.
Cleanup of bam_depths/bam_coverage commands.
Suggest 'dryrun' instead of 'dry_run'.
Use the more explicitly named MAFFT commands.

This makes the source of the binary more apparent, in case MAFFT or
one of the individual commands are missing.
Quote strings in makefile
Add/update scripts to perform profiling step.
Cleanup / check that BAMs are sorted.

Note that the check is not done based on the header, as this may
be missing (samtools sort) or wrong.
Parallelize a bit.
Fix naming to match C/L usage.