not overwrite existing file if same as tar entry (#3)

* Upgrade Jena version to 3.16.0 (vivo-project#196)

Related to: https://jira.lyrasis.org/browse/VIVO-1943

* remove example-settings.xml
* update home directory untar non-destructive
* checksum digest to retain modified files
* compare checksum from digest with existing file
* overwrite files that have not changed
* add command to manually generate checksum digest
* simplify parsing checksum digest using pattern
* do not overwrite file if same as already exists

Co-authored-by: Andrew Woods <awoods@lyrasis.org>
Co-authored-by: Andrew Woods <awoods@duraspace.org>

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/VitroHomeDirectory.java

@@ -128,13 +128,16 @@ private Map<String, String> untar(File destination) {
 
 					// reading bytes into memory to avoid having to unreliably reset stream
 					byte[] bytes = IOUtils.toByteArray(tarInput);
-					digest.put(outFilename, checksum(bytes));
+					String newFileChecksum = checksum(bytes);
+					digest.put(outFilename, newFileChecksum);
 
 					// if file already exists and stored digest contains the file,
 					// check to determine if it has changed
 					if (outFile.exists() && storedDigest.containsKey(outFilename)) {
-						// if file has not changed, overwrite
-						write = storedDigest.get(outFilename).equals(checksum(outFile));
+						String existingFileChecksum = checksum(outFile);
+						// if file has not changed and is not the same as new file, overwrite
+						write = storedDigest.get(outFilename).equals(existingFileChecksum)
+							&& !existingFileChecksum.equals(newFileChecksum);
 					}
 
 					if (write) {