Update to patched version of cppad-20140612
Squashed commit of branch 'atomic_test'

    New 'R-functions'
    -----------------
    - pgamma, qgamma, pnorm, qnorm
    - Argument 'give_log' is deprecated for all 'p' and 'q' functions.

    New macro TMB_ATOMIC_VECTOR_FUNCTION
    ------------------------------------
    - Atomic incomplete gamma function
    - Atomic inverse incomplete gamma
    - Atomic matrix inverse
    - Atomic matrix multiply
    - Atomic lgamma
    - Atomic logdet

    Other:
    ------
    - Eliminated compiler warnings
    - OS X precompile instructions
    - New example to demonstrate qgamma (transform.cpp)
Update to Eigen 3.2.2
Fixed a few more warnings:
    Warning: comparison of int and size_t in REGISTER_ATOMIC macro
    un-initialized variable warning for parallel case
    Eliminate un-used variable warning in myReverseSweep
    Eigen: Eliminate un-used typedef warning
Version and manual update
Squashed commit of the following:
    CppAD: Apply changeset_3372.diff
    - More CSkipOp related fixes
    CppAD: Apply changeset_3370.diff
    - CSkipOp related bug fixes
    CppAD: Apply changeset_3367.diff
    - Fix optimize user atomic function
    CppAD: Apply changeset_3359.diff
    - Fix invalid optimization of discrete operator (DisOp)
Atomic matrix exponential
Eliminate nan gradients caused by code not affecting the likelihood
Fix broken checkpoint macro
Add expm to precompilation
Merge pull request #52 from kaskr/testing

TMB version 1.1
Remove garbage folder