The target to produce an intermediate .aux file for latex documents
was removed in 071d7b5c to simplify the build without taking the overall
docs/ makefile into account. The latter relies on a destinct target for
.aux files.
This commit adds it back but makes sure that failed attempts to build it
still get retried by using pdflatex' drafmode (which does not write the
PDF file itself).

Also, fix some other minor issues in the makefile and the generation of
the directory of acronyms.

 - links to footnotes were fixed by deferring the loading of hyperref until
   after footmisc.
 - some cross-document links were wrong

And some other minor refinements

 - cover page:
    * remove explicit copyright notice
    * add same acknowledgment as in papers
 - use a single main makefile
 - move together common images
 - set image search path to common_tex/img
 - include a unified tex header file

 - add detailed installation instructions
 - refine appendix
 - various smaller refinements and style changes

 - add captions and change references
 - refine formatting

Addresses issue #33.