Show type of values that do not meet expectations in makefiles.
Fix for location of duplication checks file.
Cleanup of BAM makefile parsing.

Also relaxed some checks:
 - Allow the same target names, if the destinations differ (typically
   the case with multiple makefiles in different directories, and
   no value set with --destination).
 - Allow files to be included in multiple targets, but issue a warning.
   Including the same file multiple times in a target is still a fatal
   error.
Minor cleanup of phylo example data generation.
Tweak node names.
Ensure that sample BAMs are indexed.