Ran bootstrap.
Fix for Intel compiler with broken __INTEL_COMPILER macro.
SNESGetFunctionNorm gone as of PETSc 3.5.0

Have to explictly call VecNorm yourself now (and if you don't
have the residual Vec available, call SNESGetFunction).
Update traffic.
Fixing the multi-key 16-bit hash function.
Adding Ryser, 2014.
Add 'only' to bootstrap step in README.
Adding improved 64-bit hash functions.

I tested this by computing 1024^3 hashes of 4 randomly-generated input
keys. No collisions were detected.
Merge branch 'hashing'
Bugfix for netcdf with newer automake

The lack of a space between the generated "fi" keyword and the
following comment character seems to have been preventing bash from
finding the end of that if block.
Regenerate configure

Regenerating with old autotools for consistency
Cleanup of variational mesh smoother

* Removing custom typedefs
* Move constructors to C file
* 'uint' is not standard C++
* built-in types need not be passed as const
* 'if(' -> 'if (', 'for(' -> 'for (', 'while(' -> 'while ('
* Clean up function prototypes
* Fixing indentation
* Use C++ style casts
Replacing C arrays with C++ objects

double* x -> std::vector<double> x
double** x -> Array2D<double> x
double*** x -> Array3D<double> x

Got rid of all dynamic memory allocation.
Declare variables when they are used.
Use const in interfaces where appropriate.
Cleaning up C interfaces.

No need to pass mesh dimension, number of nodes, number of cells, and
number of hanging edges as separate parameters.

Removed unused FILE* parameter from several functions.

Pass references instead of pointers where possible.
Converting FILE* usage to std::ofstream where possible.

Declare variables where they are used.

Replace sqrt, abs, and fabs with their std:: versions.
Merge pull request #287 from pbauman/petsc-3.5-fixes

PETSc 3.5.0 Fixes
Fixing lots of remaining spacing and formatting issues.
Miscellaneous improvements:

* Simplifying logic in minJ_BC
* Refactor readmetr to use ifstream
* Use default op=
* Fixing some numerical constants.
* Making some parameters non-const and adding accessors.
* Add error checking for fopen.
* Passing std::strings instead of char*
* Fixing up the metr_data_gen() function.
* Properly initialize _dist_norm.