initial rework to enable eigen3 per issue #174.

1. enable eigen3 in qmake build system
2. convert Transform3d and cwise() per the eigen2->eigen3 porting faq online
3. get rid of 'using namespace boost::filesystem' as it conflicts with eigen3
more eigen3 fixes.

1. finish converting 'using namespace boost::filsystem' to 'namespace fs = boost::filesystem'.

2. initial version of changes to CMakelists.txt for the regression test
modify build system to auto-detect eigen3, and fallback to eigen2
alter Mac OSX dependencies build script to get eigen version 3.1.1

This still allows the building of eigen, 2.0.17 just change the version
number at the bottom of the file.

Eigen3 requires an 'out of source' build.
restore commented-out build commands
fix bug in build script for boost
update eigen version in README. dont use alignment in dxfdata vector.
make EIGEN_DONT_ALIGN flag work. also remove warnings when using clang.
debugging failed test: throwntogethertest polygons
more debug
Revert "more debug"

This reverts commit 8f17a48e2c76e0a7a35032ff87df7b89cdcb8772.
Revert "Revert "more debug""

This reverts commit 4ef470be1f147cb33d75117716ec83c84328da25.
Revert "Revert "Revert "more debug"""

This reverts commit 94de600995a142bb0643b70f7717be3650072644.
cleaning up for pull request
Merge branch 'master' of github.com:openscad/openscad into eigen3
cleanup for pull request
rewrite Eigen detection in CMakelists. cleanup files for pull request.
look for EIGENDIR env var. (also look for EIGEN2DIR for backwards compatability)
fix small bugs in eigen build scripts
cleanup