pid doc cleanup

generated mechanism headers depend on modcc

fixed modcc->hpp dependencies

move modparser from a submodule to the repository

* only the source has been moved over and the cmake rules updated
* the tests still have to be moved

move vector library from submodul to subdirectory

Cleanup

Cleanup

Fix for warnings with latest intel compiler.

Feature/sort synapse indices

Present an ordered sequence of compartment indices
to point processes (synapses) on creation in fvm_multicell.
Required for GPU implementations.

Also:
* Change target handle for fvm_multicell to refer to actual
  (rather than offset) mechanism index.
* Split out the range/sequence utilities that were accumulating
  in `util/range.hpp` into their own header `util/rangeutil.hpp`.
  Possibly `sequtil.hpp` is a better name…
* Add range/sequence-friendly `util::sort` and `util::sort_by`.
  The latter sorts based on comparing a derived key.
* Add `util::assign_by`. Assigns after applying a transformation.
* Fix `canonical_view` for non-const ranges/sequences.
* Unit tests for `assign`, `assign_by`, `sort`, `sort_by`.

Also updates modparser to point to the latest master.

Add script for analysis of MPI profile output.

Script collates region times from JSON-formatted profile
output, presenting raw times or quartiles in CSV table.

Bugfix/gcc 4.9.3 type test workaround

Void default argument SFINAE test for presence of
type definition within in a class fails in gcc 4.9.3.

This commit uses a different SFINAE approach to work around
the compiler bug.

Feature/fvm multicell

* move from index_view to const_index_view for mechaninism
  inintialization. This allows us to pass more generic container
  types to the constructor while avoiding redundant copies
* NOTE: required update of
    * external/vector
    * external/modparser
* fixed signed-vs-unsigned comparison warning in algorithims.hpp

Note: use of non-const reference in `mechanism_catalogue::make`
is an interim solution.

small edits to pid document

add planning documents

* Fix bug in 'close' event delivery for multicell.
* Fix displacement scaling bug in gather_all_with_partition.
* Command line parameter io, reporting for new miniapp options.
* Only master rank performs command line parameter writing.
* Add test for mpi::gather_all and mpi::gather_all_with_partition.
* Extend utility of `util::assign`, `util::append`.