New method Bio::PhyloXML::Parser#closed?, and Bio::PhyloXML::Parser.open with block.

 * New method Bio::PhyloXML::Parser#closed? to check if it is closed
   or not.
 * Bio::PhyloXML::Parser.open and open_uri now can get a block.
   When a block is given, a Bio::PhyloXML::Parser object is passed
   to the block as an argument. When the block terminates, the object
   is closed.
 * Added tests about the above changes.
Test bug fix: Opened files should be closed.

 * Test bug fix: Opened files should be closed.  When finalizing writer
   tests, temporary files are not properly closed after verify reading,
   and removing the temporary files raise erro on Windows.
FuncTestCommandCall is changed to test various command-lines.

 * New file test/data/command/echoarg2.sh shell script, which acts
   like echoarg2.bat for Windows.
 * FuncTestCommandCall is changed to test various command-lines.
Test bug fix: fixed incomplete Windows platform detection.
Incompatible change: Bio::FlatFile.open and auto use binary mode

 * Incompatible change: Bio::FlatFile.open and auto use binary mode
   (binmode) unless text mode option is explicitly given.
Test bug fix: Read Sanger chromatogram files with binary mode

 * Test bug fix: Read Sanger chromatogram files with binary mode.
   Fix error/failure on Windows due to default text mode reading.
Test bug fix: use binmode to disable CR/LF conversion (fail on Windows)
Tests using network connections are moved to test/network/

 * Tests using network connections are moved to test/network/.
   * renamed: test/functional/bio/appl -> test/network/bio/appl
   * renamed: test/functional/bio/io   -> test/network/bio/io
A test class using network connection is moved under test/network/.
test/runner.rb: Run tests only in test/unit and test/functional.
Rakefile: new tasks: test-all to run all tests, etc.

 * Rakefile: new tasks: test-all to run all tests, and test-network
   to run tests in test/network.
Use binary mode to open files.
Added workaround for changes of a module name and file names to require.
regenerate bioruby.gemspec with rake regemspec.
Bug fix: rake aborted without git
Mark echoarg2.bat and echoarg2.sh as world executable
Bug fix: GenomeNet BLAST server URI changed.

 * Bug fix: GenomeNet BLAST server URI changed.
   Reported by joaocardoso via GitHub.
   ( https://github.com/bioruby/bioruby/issues/44 )
Bug fix: Bio::NucleicAcid.to_re("s") typo
Test bug fix: tests affected by the bug of Bio::NucleicAcid.to_re("s")
config files for Travis CI continuous integration service