Fixed bug where Constituent ID's in a parse were not unique.

There was a bug in s2chelper() that caused Constituent ID's to be
repeated.  s2chelper() calls itself recursively.  The 'idCounter'
parameter was being incremented and then passed by *value* instead of
passed by *reference*.  The source code had this comment, explainging
how the counter was being passed by reference:

  /**
   * i'm using int[] as a java hack for int* (pass by reference rather than value).
   */

but the current version of the code was not using this Java hack.

It looks like the bug was introduced as part of the transition from
protobufs to Thrift sometime in November 2013.

I modified s2chelper() to match the behavior of the (working) protobuf
version of the function.
Merge branch 'master' of github.com:hltcoe/concrete-agiga
Fixed bug introduced in previous commit with creating parse trees

My previous commit fixed the issue with constituent ID's being
repeated for a parse tree, but the parse "trees" that were being
created weren't actually trees.

The Thrift version of s2chelper() should now work as well as the
protobuf version of the function worked.
Merge in Craig's changes