William Stein's Status Report for Sage Days 12

I fixed the following bugs:

#1234 -- analytic_rank crashes
#3544 -- PermutationGroup.is_transitive is broken
#4274 -- assertion failure in rank for elliptic curves
#1867 -- factoring multivariate polynomials over finite fields is broken in Singular

#4818 -- bug in list_plot3d -- invalid index?
#2858 -- parametric_plot3d throws an error when the sum of the components cancels a variable

#4029 -- sage-env kills the shell when called from "wrong" directory
#773 -- SAGE drops . from path
#5045 -- sage's "make check" should check that the sage build flags (in sage-flags.txt) are right
#5041/4955 -- make it so the magma .sig files in extcode don't get written there by magma
#5044 -- on some systems mwrank dumps core and crashes on exit when run under pexpect
#4936 -- massive bloat: make something delete everything in ~/.sage/gap > 1 week old and untouched

#4588 -- doctest -- get rid of the "feature" where docstrings with require, optional, and package all in them are automatically marked optional
#5068 -- hange_ring fails for polynomials over finite fields in many cases
#4665 -- sage/misc/cython.py creates file sage/misc/hello.spyx in tree while doctesting
#3871 -- do not save pngs in SAGE_ROOT; extending #3759