TMB version 1.1

* Update to cppad-20140612

* Update to Eigen 3.2.2 (solved all 32 bit issues)

* 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 atomic functions
    - 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)

* Fixed 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 (expm)

* Eliminate nan gradients caused by code not affecting the likelihood