Repair Failed Test Case in Integration, check PMD and refactor some codes in Shell,UniqTool,WcTool
Merge branch 'master' of https://github.com/azatris/cs4218

# By Silver Taza
# Via Silver Taza
* 'master' of https://github.com/azatris/cs4218:
  Added TODOs for mostly Javadocs, cleaned up lots of code, added consistency

Conflicts:
	test/sg/edu/nus/comp/cs4218/integration/IntegrationTestingTwoOrMorePipes.java
Add more details for javadocs
Merge branch 'master' of https://github.com/azatris/cs4218

# By Silver Taza (3) and Mingxia Liu (2)
# Via Mingxia Liu (1) and Silver Taza (1)
* 'master' of https://github.com/azatris/cs4218:
  Additional documentation for a code segment that we did not write
  Ls tool test javadocs added
  Grep Tool test javadocs added
  no message
  Small modification