[Pamgen] Don't repeat Pamgen headers for Pamgen_extras

Bug #6186.
Disabling STK in automated testing

STK has been broken in the build on the CASL Fissile machines for a long time,
since the update of STK from SIERRA.  Basically we are getting a lot of build
errors in STK being reported to CDash.

Also, I am hoping that disabling STK will speed up the build of Trilinos so
that we don't timeout the MPI_RELEASE_GCC build after 5 hours like is occuring
now.
[MueLu] don't install Tpetra adapter headers twice

See bug #6186.
[Anasazi] Don't install AnasaziTpetraAdapter.hpp twice

See bug #6186.
Changed algorithm's partition method's argument back to RCP.
Made argument lists of order() and color() match notes from 4/21/2014
coding day.
This change also removes warnings reported by Hu.
Added virtual destructor to avoid undefined behavior (and compiler warnings)
when deleting a base class.
Problem reported by Noel Belcourt
ML: print more info about eigenvalue estimate

For PrintLevel > 5, print whether eigenvalue estimate is recalculated
for prolongator smoothing, and which method is being used.
Also fixed a couple warnings about mixing declarations and code.
MueLu: option to recalc max eig for smoo prolong.

Added two options to SaPFactory:
  1) force recalculation of max eigenvalue estimate
  2) specify max number of iterations of power method.
Defaults are no (use cached estimate) and 10 (the previously hard-wired
number of iterations.)
MueLu: header cleanup

1st pass through with include-what-you-use tool
MueLu: header cleanup

2nd pass through with include-what-you-use tool
MueLu: changing calls to TimeMonitor::summarize()

Changing all MueLu tests/examples to set ignoreZeroTimers=true in calls
to Teuchos::TimeMonitor::summarize().  Related to commit e745b05d.

The effect is that processes that either have a hard zero for a
timer (unlikely) or don't have a timer won't be used in calculating the
global stats.  This will make the min, averages, and averages per
iteration more meaningful for us.
MueLu: move WriteData to standalone function

There is no reason WriteData needed to be a member of HierarchyManager, much
less private.  This way, anyone can call it.  Item #23 in Effective C++
(3rd edition).
MueLu: allow mesh stretching in RAPScalingTest
MueLu: fixing exception in ScalingTestParamList

A catch in the MueLu scaling test was not printing the actual exception
message thrown by Belos' solve.
Ifpack2: enabling Amesos2 in overlapped subdomains

Enabling the use of Amesos2 solvers as subdomain solves in overlapping
additive Schwarz.  I used the same idea of local filtering for the
sparse matrix, solution, and RHS vectors, as is done in
Ifpack2::Details::DenseSolver.

I've only tested SuperLU so far.
Ifpack2: fix two compiler warnings
Ifpack2: fix Amesos2Wrapper inner solve descr.
Amesos2: add short description for SuperLU

Mostly for the ILUTP options.
Ifpack2: add parameter list control of SuperLU

Pass along parameter list options to Amesos2's interface to SuperLU.
In particular, you can now enable SuperLU's ILUTP.