Including .ini, .m files, .py in distribution.

[donnaaboise]

Add any extra files to the EXTRA_DIST flag, i.e. in the swirl example, we have added :

EXTRA_DIST += \
	applications/clawpack/advection/2d/swirl/fclaw_options.ini \
	applications/clawpack/advection/2d/swirl/regression.ini \
	applications/clawpack/advection/2d/swirl/afterframe.m \
	applications/clawpack/advection/2d/swirl/setplot2.m \
	applications/clawpack/advection/2d/swirl/swirl.ipynb \
	applications/clawpack/advection/2d/swirl/make_plots.py

The problem is that this is only conditionally included, since the Makefile.am is only conditionally included. As a result, it is NOT included in a distribution. To get around this, we need to make sure that EXTRA_DIST is always included (not only conditionally). As a work-around, these can be included AFTER the conditional compile in Makefile.apps

[cburstedde]

A fix would be to always include all Makefile.ams, and use the conditional checks inside each Makefile.am.