featurecounts: fix unused parameters

[bernt-matthias]

tool defined a parameter --countSplitAlignmentsOnly that was unused in
the command section. Even worse such a parameter does not exist on the
CLI, but:

  --splitOnly         Count split alignments only (ie. alignments with CIGAR
                      string containing 'N'). An example of split alignments is
                      exon-spanning reads in RNA-seq data.

  --nonSplitOnly      If specified, only non-split alignments (CIGAR strings do
                      not contain letter 'N') will be counted. All the other
                      alignments will be ignored.

this has been fixed.

Furthermore some parameters from the large Advanced options section
have been moved to a new Read filtering options section (as suggested
by the nice featureCounts help output).

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