Besides that these files are never created (I'm assuming @codebrainz is right and it's a left-over from one of his stuff), the python script only opens ever opens the xml subdirectory, and in their it uses the doxygen output (combine.xslt) to learn which other xml it has to parse. Are you sure this still happens? What's the exact error?

  GEN      geany-gtkdoc.h
Traceback (most recent call last):
  File "../../scripts/gen-api-gtkdoc.py", line 415, in <module>
    sys.exit(main(sys.argv))
  File "../../scripts/gen-api-gtkdoc.py", line 352, in main
    root = transform(doc)
  File "src/lxml/xslt.pxi", line 579, in lxml.etree.XSLT.__call__ (src/lxml/lxml.etree.c:187342)
  File "src/lxml/lxml.etree.pyx", line 322, in lxml.etree._ExceptionContext._raise_if_stored (src/lxml/lxml.etree.c:11069)
lxml.etree.XSLTApplyError: Cannot resolve URI xml/interface_8dox.xml

Fetching interface.dox and interface.xslt from @codebrainz's repo https://github.com/codebrainz/geany/blob/50f76094b06a2d7ae2a9ab7f1f594c052a479078/doc/

But forget it, it's not your PR's fault but the $(srcdir)/*.dox entry in doxygen_sources that trigger inclusion of interface.dox, which then refers non-generated things apparently.

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