Update .gitignore; improve documentation

Add the `files` directories to the .gitignore to prevent them from being
committed again. Update the readme with the latest command line options,
and revise method documentation to match implementation.

.gitignore

@@ -1,3 +1,5 @@
 *.log
 output.*.txt
 .vscode
+files
+files.*/

README.md

@@ -26,14 +26,16 @@ arguments cannot be passed to a Makefile target.
 ## Options
 
 ```
+  -output string
+        output file (default is stdout)
   -path string
-    	path to the file pool (default "files")
+        path to the file pool (default "files")
   -prefix
-    	use '[doc ###]' prefix for output
+        use '[doc ###]' prefix for output
   -threshold float
-    	similarity threshold (default 0.5)
+        similarity threshold (default 0.5)
   -verbose
-    	enable verbose logging
+        enable verbose logging
   -workers int
-    	number of workers to use (default 2*<number-of-cores>)
+        number of workers to use (default 2*<number-of-cores>)
 ```

main.go

@@ -311,9 +311,10 @@ func (dm *DocumentManager) maybeAssociateFileWithDocument(workItem WorkItem, wor
 	}
 }
 
-// compareFiles computes how much two files overlap, on a scale
-// of 0 to 1 by iterating through the files and identifying lines
-// that are duplicated.
+// compareFiles computes how much two files overlap on a scale of 0 to 1 by
+// iterating through the files and calculating a similarity score that's based
+// on the number of line-centric differences between the contents of the two
+// files.
 func (dm *DocumentManager) compareFiles(f1Number, f2Number int) (float64, error) {
 	f1, err := dm.fcc.GetFileContents(f1Number)
 	if err != nil {