Cleanup/consolidation/expansion of *Utils classes

* IoUtils.java
    remove class that confusingly-overlaps with commons IOUtils; move remaining methods to ArchiveUtils or archive's FileUtils
* ArchiveUtils.java, FileUtils.java
    receive relocated methods; eliminated deprecated or unused methods
* JSONUtils.java
    new class to collect common JSON actions
* Iteratorable.java
    wrap Iterator as Iterable for foreach usage
* (many)
    update to use alternate utils methods

modules/src/main/java/org/archive/modules/fetcher/AbstractCookieStorage.java

@@ -35,7 +35,7 @@ import java.util.logging.Logger;
 
 import org.apache.commons.httpclient.Cookie;
 import org.archive.spring.ConfigPath;
-import org.archive.util.IoUtils;
+import org.archive.util.ArchiveUtils;
 import org.springframework.context.Lifecycle;
 
 /**
@@ -154,7 +154,7 @@ public abstract class AbstractCookieStorage
         } catch (IOException e) {
             LOGGER.log(Level.WARNING,e.getMessage(), e);
         } finally {
-            IoUtils.close(raf);
+            ArchiveUtils.closeQuietly(raf);
         }
     }
     

modules/src/main/java/org/archive/modules/recrawl/PersistProcessor.java

@@ -41,7 +41,6 @@ import org.archive.modules.CrawlURI;
 import org.archive.modules.Processor;
 import org.archive.util.ArchiveUtils;
 import org.archive.util.FileUtils;
-import org.archive.util.IoUtils;
 import org.archive.util.OneLineSimpleLogger;
 import org.archive.util.SURT;
 import org.archive.util.bdbje.EnhancedEnvironment;
@@ -301,10 +300,10 @@ public abstract class PersistProcessor extends Processor {
         } else {
             BufferedReader persistLogReader = null;
             if (sourceFile.isFile()) {
-                persistLogReader = IoUtils.getBufferedReader(sourceFile);
+                persistLogReader = ArchiveUtils.getBufferedReader(sourceFile);
             } else {
                 URL sourceUrl = new URL(sourcePath);
-                persistLogReader = IoUtils.getBufferedReader(sourceUrl);
+                persistLogReader = ArchiveUtils.getBufferedReader(sourceUrl);
             }
             count = populatePersistEnvFromLog(persistLogReader, historyMap);
         }

modules/src/main/java/org/archive/modules/writer/MirrorWriterProcessor.java

@@ -50,7 +50,7 @@ import org.archive.io.ReplayInputStream;
 import org.archive.modules.CrawlURI;
 import org.archive.modules.Processor;
 import org.archive.net.UURI;
-import org.archive.util.IoUtils;
+import org.archive.util.FileUtils;
 
 /**
    Processor module that writes the results of successful fetches to
@@ -399,7 +399,7 @@ public class MirrorWriterProcessor extends Processor {
                 destFile = new File(baseDir + File.separator + mps);
                 File parent = destFile.getParentFile();
                 if (null != parent) {
-                    IoUtils.ensureWriteableDirectory(parent);
+                    FileUtils.ensureWriteableDirectory(parent);
                 }
             } else {
                 URIToFileReturn r = null; // Return from uriToFile().