Improve count_points

I use Harvey's algorithm already in sage to speed up the computations.
Refactor point counting code for hyperelliptic curves.
First bunch of fixes and missing examples.
Switched an old patch to git and made doctests pass.
Turn off points precomputing for reflexive polytopes.
Deprecated vertices().
Made doctests pass again.
Deprecated points() and fixed doctests.
Deprecate constructing lattice polytopes from matrices as well.
Deprecate projective_space polytope.
Rebase on top of #15108.
rebase to 6.0
Initial setup.
Merge branch 'develop' into public/combinat/crystals/catalog

* develop: (107 commits)
  Updated Sage version to 6.1.beta5
  Don't use "missing"
  trac 15265: various changes, finishing review.
  allow disabling of maintainer mode
  trac 15265: Additional change to farey.cpp.
  trac 15265: Minor changes to farey_symbol.pyx
  trac 15265: Minor changes to sl2z.cpp and sl2z.hpp.
  trac 15265: Minor changes to farey.cpp and farey.hpp.
  Run "missing" using bash
  fix tarball url
  trac 15265: Add some further examples and one test to _acton_ of elements of arithmetic groups.
  Source sage-env inside configure
  Improved Karatsuba: more thorough tests
  bootstrap configure: small fixes
  make saving of the confball optional in bootstrap
  fix typos in SPKG.txt
  also commit changes to confball in sage-update-version
  add a SPKG.txt file
  rename to bootstrap, run during version bump
  trac 15265: correct mistakes done while converting to git branch.
  ...
Merge branch 'develop' into public/combinat/crystals/catalog

* develop: (120 commits)
  Updated Sage version to 6.1.rc0
  only use CONFVERSION after it has been incremented
  note that the E6->A5 rule is now implemented
  document the glibc bug workaround patch
  Avoid scanf instead of just ignoring rest of file
  bump confball version
  fix for the m4_divert_push error
  sage-clone-source: allow downloading the configure tarball
  Require autoconf 2.64
  revised thematic tutorial regarding maximal_subgroup(s) method
  reference: branching_rules: minor fixup
  bump confball version
  removed bogus commits
  LinearMatroid.is_field_equivalent now tests if self is other before calling LinearMatroid._is_field_isomorphism.
  implemented maximal_subgroup(s) as a WeylCharacterRing method etc.
  Updated Sage version to 6.1.beta6
  Do not use the GNU extension chmod --recursive
  Workaround for glibc-2.18 scanf bug when building ATLAS
  Added  free_group and finitely_presented_group
  Made the repr sorted for the rules.
  ...
Merge branch 'develop' into public/combinat/crystals/catalog

* develop: (188 commits)
  Updated Sage version to 6.2.beta1
  Use posix locale for regex
  Let ncurses build again on Solaris.
  Tweaks for speed in sparse graph backend for #15715.
  Updated Sage version to 6.1.1
  trac #14508: better now?
  Trac 14508: bugfix in jordan_form
  Update README.txt re installation with OS X Mavericks
  Fix test for empty string in FLINT build system.
  Update to version 0.10.8.2
  Update sagenb to 0.10.8.1
  Replace two more "except StandardError:"
  Updated Sage version to 6.2.beta0
  Fix documentation syntax
  GSL FFT: indentation (& related) fixes in docstrings
  Minor documentation fixes.
  #Documentation for gsl/fft.pyx
  #10058: Segfault in backward and inverse FFT for 2**n elements
  Regression test for #7475
  Trac #8499: reviewer patch
  ...
Merge branch 'develop' into public/combinat/crystals/catalog

* develop: (58 commits)
  Updated Sage version to 6.2.beta2
  fix doctest error
  Limit the GAP command line history
  integrate better with Integer.is_prime
  Combine ECM-GMP with Baillie-PSW for prime factorization
  Cleaned up documentation and formatting.
  add doctesr
  Trac 15262: fix combine function
  trac #15810: The graph data structures may have a ._directed but no .directed
  ignore randomness in assertion
  trac #15810: Immutable directed graphs should know that they are directed
  Trac 15166: regression test
  Fix representation of RIF elements with large exponent
  docbuilding: suppress warnings during latex build
  workaround for the utf8 code points in the Sage banner
  Trac 15798: fix mwrank doctest for Solaris
  do not abbreviate 3.99999... to 3.99 with # abs tol 1e-2
  setuptools: export PYTHON_EGG_CACHE and silence a warning about it
  Remove .hgignore files
  PARI: fix pow, mod and shift operators
  ...
Adjusted several enumerative functions BasisExchangeMatroid to separately handle the fringe
case where the ground set is empty.
Renamed catalog files.
Starting to deprecate from global namespace.