Redefining a typedef is an error prior to C11
Fix convert.h dependencies
Move test_rename_chrs() output files out of $$opts{tmp}

Evidence of test failure evaporates if it is written to the tmp
directory (which is cleaned when the script ends), so write the files
to $$opts{path} like all the others.  Unlike the others, rename.out.tmp
is created each time in test_rename_chrs() rather than prewritten,
and is usually deleted afterwards (except when renaming tests fail).
Merge convert, filter, and rename-chrs branches

While merging, fixed merge conflicts left behind in bcftools.1,
fixed whitepace (no tabs or trailing spaces please!), reformatted
licensing boilerplate on new files to match existing files.
Merge branch 'develop' of git://github.com/samtools/bcftools into feature/idxstats