It's explained in the description of commit cf8c3a84 -
authority-koha-indexdefs.xml is the master set of indexing
definitions, and it expresses those definitions (relatively)
compactly.  authority-zebra-indexdefs.xsl is what is actually used by
Zebra to transform the MARCXML authority record into XML representing
the terms to be stored  in Zebra's indexes.  To generate that
authority-zebra-indexdefs.xsl, you use koha-indexdefs-to-zebra.xsl
XSLT, e.g.,

xsltproc koha-indexdefs-to-zebra.xsl authority-koha-indexdefs.xml >
authority-zebra-indexdefs.xsl 

Of course, storing both authority-koha-indexdefs.xml and
authority-zebra-indexdefs.xsl in the repository violates the guideline
that a version control repository shouldn't contain derived files,
just source files and build scripts.  Mea culpa.  One fix would be to
drop authority-zebra-indexdefs.xsl from Git and update the installer
scripts to generate it when needed.