Various "make distcheck" and portability fixups 2nd part

doc/examples/Makefile.am:

* Use $(VAR), not @VAR@

* Use $(MKDIR_P) instead of $(mkinstalldirs), as the latter is an
* obsolete
  name

* Added $(srcdir) qualification to the various test program invocations
* in
  the "tests" target. More work is needed here (notably, when the
  reference output contains the path to the input file), but this gets
  things a lot closer to working correctly in an out-of-source build.

doc/examples/reader4.res:

* Added "./" path qualifiers so that the reader4 test continues to pass
  cleanly for in-source builds

python/tests/Makefile.am:

* Symlink in test input files for out-of-source builds