Payu

- Top-level models (i.e. models with submodels) are now handled as
independent models, with their own configuration elements (e.g. input
directory, etc.) This allows configuration files to be shared more easily
across submodels.

Much of this work is ongoing, and this should be seen as a progressive
step, rather than the final product.

- `ocean_mask_table` has been added to the MOM driver as an optional config
file.

- Optional configuration files are now (perhaps temporarily) copied to the
`work_input_path` rather than `work_path`. This is solely to accommodate
the `ocean_mask_table` in ACCESS-OM2. This probably needs to be
restructured better in the future.

- Missing restart files in the old ACCESS are now handled more safely. If
a restart file is missing, it will conditionally check the prior output.

- CICE output file permissions are correctly set to be user-writeable.

- Hyperthreading is now correctly removed from collation jobs. There was
some poor handling of the optional space betweel `-l` and the flag
contents which has been fixed.

New model support:
- YATM
- ACCESS-OM2

NOTE: The ACCESS-OM2 driver currently overrides most of the intrinsic
Payu driver structure, and will probably be rewritten at some stage.

- The largely unused `exe_prefix` config setting was basically unusable
since it was not passed to the model object. This change now passes it
to the model object, which handles the executable command.

- Environment variable corruption of bash functions by PBS is now only
applied if the `BASH_FUNC_module()` variable is present. This prevents
failing under tcsh.
- Numerical job names should now work correctly
- Bash-like environment variable substitution can now be used in MPI flags.
This feature may be extended to other components if necessary.
- Multiple runs per PBS submission now supported (`runspersub`)
- Safer import of f90nml
- ACCESS-OM2:
- Necessary configuration files are now copied to the restart
directory.
- CICE namelists now search in the prior output path if absent from the
prior restart path
- Safer CICE restart cleanup
- FMS:
- Collation by mppnccombine will now report a nonzero error code if any
of its pool threads fails, which will halt resubmission.

- Remote synchronization of run experiment with github repository
- Error logs are now captured and archived separately from successful runs
- PBS and error logs are now saved in the archive directory
- Basic OpenMP support
- FMS collation default flag update (netCDF4)
- Error code reporting from FMS collation
- OASIS namcouple cleanup (Nic Hannah)

New dependencies:
- requests[security] (for github sync support)

New model support:
- Q-GCM
- CICE 5

Bug fixes:
- Calendar leap year support (Nic Hannah)
- Payu module pathname
- Protect environment variables with '\n' from corruption by PBS Pro
- CICE restart cleanup (Nic Hannah)

- `payu setup` and `payu archive` commands now available
(c/o Aidan Heerdegen)
- Basic support for NEMO
- `platform` configuration now available to set per-node CPU and RAM
- Enable Lustre IO striping with `stripedio` config flag
- Git-based logging of job submissions is now enabled by default
- Basic (and incomplete) testing framework now available
- Several bugfixes related to repeatable runs and submodel testing

- Partially committed node flags (`npernode`) updated to new syntax
- Non-directories in archive (e.g. symbolic links) are not deleted
- Improved single-core MITgcm support
- MITgcm runtimes can now be set in time, rather than just timesteps
- `payu build` now ignores user .gitconfig settings
- Some profiler cleanup (openspeedshop moved to Profiler class)
- Minimal WAVEWATCH III support
- A non-functional test suite was started, please add to it!

- Multithreaded collation (c/o Aidan Heerdegen)
- Improved CICE and ACCESS support (c/o Nicholas Hannah)
- Explict output collation path (c/o Aidan Heerdegen)
- Default jobname is not set to control path directory name
- repeat runs (repeat: True) now delete any restart files
- Profiler driver class introduced (not yet adopted for all)
- Documentation update (incomplete)