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

engine/src/main/java/org/archive/crawler/frontier/BdbWorkQueue.java

@@ -26,7 +26,6 @@ import java.util.logging.Logger;
 
 import org.archive.modules.CrawlURI;
 import org.archive.util.ArchiveUtils;
-import org.archive.util.IoUtils;
 
 import com.sleepycat.je.DatabaseEntry;
 import com.sleepycat.je.DatabaseException;
@@ -73,7 +72,7 @@ implements Serializable {
             return queues.deleteMatchingFromQueue(match, classKey,
                 new DatabaseEntry(origin));
         } catch (DatabaseException e) {
-            throw IoUtils.wrapAsIOException(e);
+            throw new IOException(e);
         }
     }
 
@@ -84,8 +83,7 @@ implements Serializable {
                 .getWorkQueues();
              queues.delete(peekItem);
         } catch (DatabaseException e) {
-            e.printStackTrace();
-            throw IoUtils.wrapAsIOException(e);
+            throw new IOException(e);
         }
     }
 
@@ -146,7 +144,7 @@ implements Serializable {
                         curi.toString());
             }
         } catch (DatabaseException e) {
-            throw IoUtils.wrapAsIOException(e);
+            throw new IOException(e);
         }
     }
     

engine/src/main/java/org/archive/crawler/frontier/FrontierJournal.java

@@ -32,7 +32,7 @@ import org.archive.crawler.framework.Frontier;
 import org.archive.io.CrawlerJournal;
 import org.archive.modules.CrawlURI;
 import org.archive.modules.deciderules.DecideRule;
-import org.archive.util.IoUtils;
+import org.archive.util.ArchiveUtils;
 import org.json.JSONObject;
 
 /**
@@ -191,7 +191,7 @@ public class FrontierJournal extends CrawlerJournal implements Checkpointable {
         DecideRule scope = (scopeIncludes) ? frontier.getScope() : null;
         FrontierJournal newJournal = frontier.getFrontierJournal();
         
-        BufferedReader br = IoUtils.getBufferedReader(source);
+        BufferedReader br = ArchiveUtils.getBufferedReader(source);
         String read;
         int lines = 0; 
         try {
@@ -268,7 +268,7 @@ public class FrontierJournal extends CrawlerJournal implements Checkpointable {
         try {
             // Scan log for all 'F+' lines: if not alreadyIncluded, schedule for
             // visitation
-            br = IoUtils.getBufferedReader(source);
+            br = ArchiveUtils.getBufferedReader(source);
             try {
                 while ((read = br.readLine())!=null) {
                     qLines++;

engine/src/main/java/org/archive/crawler/frontier/precedence/PrecedenceLoader.java

@@ -30,7 +30,7 @@ import java.util.Iterator;
 import java.util.Map;
 
 import org.archive.modules.recrawl.PersistProcessor;
-import org.archive.util.IoUtils;
+import org.archive.util.ArchiveUtils;
 import org.archive.util.bdbje.EnhancedEnvironment;
 import org.archive.util.iterator.LineReadingIterator;
 
@@ -119,7 +119,7 @@ public class PrecedenceLoader {
         
         if(source.isFile()) {
             // scan log, writing to database
-            BufferedReader br = IoUtils.getBufferedReader(source);
+            BufferedReader br = ArchiveUtils.getBufferedReader(source);
             Iterator iter = new LineReadingIterator(br);
             while(iter.hasNext()) {
                 String line = (String) iter.next(); 

engine/src/main/java/org/archive/crawler/util/RecoveryLogMapper.java

@@ -41,7 +41,7 @@
 package org.archive.crawler.util;
 
 import org.archive.crawler.frontier.FrontierJournal;
-import org.archive.util.IoUtils;
+import org.archive.util.ArchiveUtils;
 
 import java.io.File;
 import java.io.LineNumberReader;
@@ -118,7 +118,7 @@ public class RecoveryLogMapper {
     protected void load(String recoverLogFileName)
             throws java.io.FileNotFoundException, java.io.IOException,
             SeedUrlNotFoundException {
-        LineNumberReader reader = new LineNumberReader(IoUtils
+        LineNumberReader reader = new LineNumberReader(ArchiveUtils
                 .getBufferedReader(new File(recoverLogFileName)));
         String curLine = null;
         while ((curLine = reader.readLine()) != null) {