Integration; Summarize methods

AMISummaryTest

## org.contentmine.ami.tools.AMISummaryTest#testFlattenMethods Summarizes methods in battery10 corpus.

		String root = "methods";
		String project = "summarizeProject/";
		File expectedDir = new File(TEST_BATTERY10+"."+"expected", project);
		File targetDir = new File(TARGET_DIR, project);
		CMineTestFixtures.cleanAndCopyDir(TEST_BATTERY10, targetDir);
		String sections = "sections/body/"+root;
		String cmd = "-vvv"
				+ " -p "+targetDir
//				+ " --output " + "/sections/body/"+root
				+ " --output " + sections
				+ " summary "
				+ " --glob **/PMC*/sections/*_body/*_methods/**/*_p.xml"
				+ " --flatten"
			;
		AMI.execute(cmd);
		File outputFile = new File(targetDir, "_summary/"+sections);
		Assert.assertTrue("output "+outputFile, outputFile.toString().endsWith("ami3/target/summary/summarizeProject/_summary/sections/body/methods"));
		System.out.println("target "+targetDir);
		AbstractAMITest.compareDirectories(targetDir, expectedDir);