README: minor update to reference MANUAL.md in doc subdir.
RnaChipIntegrator v0.4.1: add --pad option for output of ChIP-seq-centric analyses.

--pad affects the output of NearestTranscriptsToPeakEdge and NearestTSSToPeakEdge
(i.e. ChIP-seq-centric) analyses, adding additional empty lines where fewer than
MAX_CLOSEST transcripts (set by --number) are found for a peak.