PGMReader: pixel data of PPM files is interleaved (issue #1263).
PGMReader: use whitespace instead of lines to delimit entries on file header.

The netpbm file formats has 2 or 3 entries on the header delimited by
whitespace. The current implementation only recognized individual lines.
It is possible that there's no newlines in the entire file which caused
the reader to blow. In adition, this formats also allows for comments
anywhere before the raster data while currently they were only identified
if at the start of a line. Fixed all this by making use of StreamTokenizer.
PGMReader: set metadataComplete to false since comments and stack are ignored.

Because the comments in the file are discarded during read, we are confident
that we there's metadata being discarded. Set metadataComplete to false.
The netpbm file formats support image stacks since July 2000 but only the
first image is actually being read.
Merge pull request #1285 from sbesson/memoizer_getmemofile

Fix Memoizer.getMemoFile(id) when directory is the root path
merge develop -Dorg -Ssuccess-only: PR 1154 (Leica: prevent exception when linking EmissionFilter)
merge develop -Dorg -Ssuccess-only: PR 1268 (multiple netpbm fixes)
merge develop -Dorg -Ssuccess-only: PR 1279 (travis: Build with Oracle JDK 8)
merge develop -Dorg -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1249 PremyslFiala 'ND2 - Bug fixes' (user: PremyslFiala)
  # PR 1265 qidane 'New units' (label: exclude breaking)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 1252 imunro 'Add Example code or writing Plate data to ome-tiff.' (status: pending)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 1290 rleigh-dundee 'cmake: CompilerChecks: Correct standard warnings' (status: error)
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (label: exclude)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
Updating 9d2af4a..e4d1ba8
Previously merged:
  # PR 1285 sbesson 'Fix Memoizer.getMemoFile(id) when directory is the root path'

Merged PRs:
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter'
  # PR 1268 carandraug 'multiple netpbm fixes'
  # PR 1279 rleigh-dundee 'travis: Build with Oracle JDK 8'

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Update auto-generated documentation

Repository: snoopycrimecop/bioformats

Generated by BIOFORMATS-5.1-merge-docs-autogen#21 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.1-merge-docs-autogen/21/)