Using deprecated Apache Commons CLI classes

[psybers]

    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/BoaMain.java:27: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] import org.apache.commons.cli.PosixParser;
    [javac]                              ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/compiler/BoaCompiler.java:44: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] import org.apache.commons.cli.PosixParser;
    [javac]                              ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/datagen/BoaGenerator.java:25: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] import org.apache.commons.cli.PosixParser;
    [javac]                              ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/evaluator/BoaEvaluator.java:30: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] import org.apache.commons.cli.PosixParser;
    [javac]                              ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/runtime/BoaRunner.java:23: warning: [deprecation] OptionBuilder in org.apache.commons.cli has been deprecated
    [javac] import org.apache.commons.cli.OptionBuilder;
    [javac]                              ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/runtime/BoaRunner.java:26: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] import org.apache.commons.cli.PosixParser;
    [javac]                              ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/BoaMain.java:49: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac]                 final CommandLine cl = new PosixParser().parse(options, new String[] { args[0] });
    [javac]                                            ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/compiler/BoaCompiler.java:394: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] 			cl = new PosixParser().parse(options, args);
    [javac] 			         ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/compiler/BoaCompiler.java:433: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] 			cl = new PosixParser().parse(options, args);
    [javac] 			         ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/datagen/BoaGenerator.java:46: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] 			cl = new PosixParser().parse(options, args);
    [javac] 			         ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/evaluator/BoaEvaluator.java:78: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] 				final CommandLine cl = new PosixParser().parse(options, args);
    [javac] 				                           ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/runtime/BoaRunner.java:116: warning: [deprecation] OptionBuilder in org.apache.commons.cli has been deprecated
    [javac] 		options.addOption(OptionBuilder.withLongOpt("job")
    [javac] 		                  ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/runtime/BoaRunner.java:121: warning: [deprecation] OptionBuilder in org.apache.commons.cli has been deprecated
    [javac] 		options.addOption(org.apache.commons.cli.OptionBuilder.withLongOpt("ast")
    [javac] 		                                        ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/runtime/BoaRunner.java:126: warning: [deprecation] OptionBuilder in org.apache.commons.cli has been deprecated
    [javac] 		options.addOption(org.apache.commons.cli.OptionBuilder.withLongOpt("comments")
    [javac] 		                                        ^
    [javac] /Users/rdyer/boa/compiler-master/src/java/boa/runtime/BoaRunner.java:139: warning: [deprecation] PosixParser in org.apache.commons.cli has been deprecated
    [javac] 			line = new PosixParser().parse(options, args);

[psybers]

Hadoop 1.2.1 (what Boa currently runs on) has it's own version of apache CLI 1.2 and thus we can not currently upgrade to 1.3. The changes in 93e9f86 are reverted.