Changes

configure.ac: internalise CoDiPack/MediPack flags for --enable-ad

* Adds --enable-ad plus --with-{codi,medi}pack-dir options.
* When --enable-ad is chosen:
    - Defines ISSM_USE_AD for conditional compilation.
    - Injects include paths, library paths and –lcodi/–lmedi into
      AM_CPPFLAGS, AM_LDFLAGS and LIBS so every sub-dir picks them up.
    - Automatically disables PETSc to avoid an impossible combo.
* Emits AM_CONDITIONAL(USE_AD) for any Makefile.am that still wants it.
* Leaves all Makefile.am files untouched; the Spack recipe no longer
  needs setup_build_environment() hacks.

Doing this upstream means:
  • Classic builds behave exactly as before.
  • AD builds work out-of-the-box for Spack, EasyBuild or manual
    ./configure invocations.

style changes and revert

issm options repetition removed
 (commit: 5573a54)