[FIX] Making BED coordinates 0-based.

Often, text-based formats use 1-based formats but BED uses 0-based formats.
[DOC] Beefing up documentation for NameStoreCache.

Includes a demo.
Merge pull request #54 from holtgrewe/feature/name-cache-dox

[DOC] Beefing up documentation for NameStoreCache.
[FEATURE] Renaming GenomicRegion::seqId => ::rID.

This is consistent with BamAlignmentRecord etc.
[API] Renaming GffRecord::tag{Name,Value} => ::tag{Names,Values}
[API] ArgParseArgument::{INPUT,OUTPUT}FILE => {INPUT,OUTPUT}_FILE

This makes the enum value name more consistent.
Merge pull request #57 from holtgrewe/feature/rename-input-output-file

[API] ArgParseArgument::{INPUT,OUTPUT}FILE => {INPUT,OUTPUT}_FILE
Merge pull request #56 from holtgrewe/feature/stream/rename-gff-tag-name-value

[API] Renaming GffRecord::tag{Name,Value} => ::tag{Names,Values}
Merge pull request #55 from holtgrewe/feature/rename-genomic-region-seq-id

[FEATURE] Renaming GenomicRegion::seqId => ::rID.
Merge pull request #53 from holtgrewe/fix/bed-to-0-based

[FIX] Making BED coordinates 0-based.
[DOC] Fixing dox such that it can be built without crashing dox.
[DOC] Starting to add documentation for stream module.

The parts that I could not write documentation for are annotated with
TODOs.  Also includes partial documentation in basic that I needed to
point to.

Plus one fix for dox.
[FEATURE,API] Refactorization of ucsc_io module.

Adding SmartFile for Ucsc format, besides others.

I/O in store module is a bit clunky.

Most of the tests were duplicates, I do not know what the original
author intended.
[FIX] Fixing initialization issues in edit environment iterators.
[FIX] Fixing misuse of append => appendValue() in rep_sep.
[FIX] Using string literal instead of string in gustaf.
[FIX] Fixing a replace() that uses a single element as the source.

Also, whitespace reformatting. The change is only in the "if (j != i)"
branch.
[FIX] Removing usage of elements-are-container feature.
[FIX] Member initialization in graph_impl_hmm.h.

Also, white space changes. The only semantic change is in initializing
data_begin and data_end in the default constructor.
[FIX] Missing member initialization in mason_variator.cpp.