Index: oak-run/src/main/java/org/apache/jackrabbit/oak/run/SegmentUtils.java
===================================================================
--- oak-run/src/main/java/org/apache/jackrabbit/oak/run/SegmentUtils.java	(revision 1746139)
+++ oak-run/src/main/java/org/apache/jackrabbit/oak/run/SegmentUtils.java	(working copy)
@@ -169,9 +169,27 @@
     }
 
     static void compact(File directory, boolean force) throws IOException {
+
+        boolean persistCM = Boolean.getBoolean("tar.PersistCompactionMap");
+        CompactionStrategy compactionStrategy = new CompactionStrategy(
+                false, CompactionStrategy.CLONE_BINARIES_DEFAULT,
+                CompactionStrategy.CleanupType.CLEAN_ALL, 0,
+                CompactionStrategy.MEMORY_THRESHOLD_DEFAULT) {
+
+            @Override
+            public boolean compacted(Callable<Boolean> setHead)
+                    throws Exception {
+                // oak-run is doing compaction single-threaded
+                // hence no guarding needed - go straight ahead
+                // and call setHead
+                return setHead.call();
+            }
+        };
+        compactionStrategy.setOfflineCompaction(true);
+        compactionStrategy.setPersistCompactionMap(persistCM);
+
         FileStore store = openFileStore(directory.getAbsolutePath(), force);
         try {
-            boolean persistCM = Boolean.getBoolean("tar.PersistCompactionMap");
             System.out.println("Compacting " + directory);
             System.out.println("    before " + Arrays.toString(directory.list()));
             long sizeBefore = FileUtils.sizeOfDirectory(directory);
@@ -181,22 +199,6 @@
 
             System.out.println("    -> compacting");
 
-            CompactionStrategy compactionStrategy = new CompactionStrategy(
-                    false, CompactionStrategy.CLONE_BINARIES_DEFAULT,
-                    CompactionStrategy.CleanupType.CLEAN_ALL, 0,
-                    CompactionStrategy.MEMORY_THRESHOLD_DEFAULT) {
-
-                @Override
-                public boolean compacted(Callable<Boolean> setHead)
-                        throws Exception {
-                    // oak-run is doing compaction single-threaded
-                    // hence no guarding needed - go straight ahead
-                    // and call setHead
-                    return setHead.call();
-                }
-            };
-            compactionStrategy.setOfflineCompaction(true);
-            compactionStrategy.setPersistCompactionMap(persistCM);
             store.setCompactionStrategy(compactionStrategy);
             store.compact();
         } finally {
@@ -205,6 +207,7 @@
 
         System.out.println("    -> cleaning up");
         store = openFileStore(directory.getAbsolutePath(), false);
+        store.setCompactionStrategy(compactionStrategy);
         try {
             for (File file : store.cleanup()) {
                 if (!file.exists() || file.delete()) {
Index: oak-segment/src/main/java/org/apache/jackrabbit/oak/plugins/segment/file/FileStore.java
===================================================================
--- oak-segment/src/main/java/org/apache/jackrabbit/oak/plugins/segment/file/FileStore.java	(revision 1746139)
+++ oak-segment/src/main/java/org/apache/jackrabbit/oak/plugins/segment/file/FileStore.java	(working copy)
@@ -866,7 +866,8 @@
         LinkedList<File> toRemove = newLinkedList();
         Set<UUID> cleanedIds = newHashSet();
         for (TarReader reader : cleaned.keySet()) {
-            cleaned.put(reader, reader.cleanup(referencedIds, cleanedIds));
+            cleaned.put(reader, reader.cleanup(referencedIds, cleanedIds,
+                    compactionStrategy));
             if (shutdown) {
                 gcMonitor.info("TarMK GC #{}: cleanup interrupted", gcCount);
                 break;
Index: oak-segment/src/main/java/org/apache/jackrabbit/oak/plugins/segment/file/TarReader.java
===================================================================
--- oak-segment/src/main/java/org/apache/jackrabbit/oak/plugins/segment/file/TarReader.java	(revision 1746139)
+++ oak-segment/src/main/java/org/apache/jackrabbit/oak/plugins/segment/file/TarReader.java	(working copy)
@@ -52,6 +52,7 @@
 
 import org.apache.commons.io.FileUtils;
 import org.apache.jackrabbit.oak.plugins.segment.SegmentGraph.SegmentGraphVisitor;
+import org.apache.jackrabbit.oak.plugins.segment.compaction.CompactionStrategy;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -737,8 +738,10 @@
 
     /**
      * Garbage collects segments in this file. First it collects the set of
-     * segments that are referenced / reachable, then (if more than 25% is
-     * garbage) creates a new generation of the file.
+     * segments that are referenced / reachable, then it creates a new
+     * generation of the file, if more than 25% is garbage. In the case of
+     * offline compaction, a new tar file will be created no matter how much
+     * garbage is detected.
      * <p>
      * The old generation files are not removed (they can't easily be removed,
      * for memory mapped files).
@@ -749,7 +752,8 @@
      * @return this (if the file is kept as is), or the new generation file, or
      *         null if the file is fully garbage
      */
-    synchronized TarReader cleanup(Set<UUID> referencedIds, Set<UUID> removed) throws IOException {
+    synchronized TarReader cleanup(Set<UUID> referencedIds, Set<UUID> removed,
+            CompactionStrategy strategy) throws IOException {
         String name = file.getName();
         log.debug("Cleaning up {}", name);
 
@@ -786,11 +790,15 @@
             removed.addAll(cleaned);
             logCleanedSegments(cleaned);
             return null;
-        } else if (size >= access.length() * 3 / 4 && graph != null) {
+        }
+        double threshold = strategy.isOfflineCompaction() ? 99 / 100 : 3 / 4;
+        if (size >= access.length() * threshold && graph != null) {
             // the space savings are not worth it at less than 25%,
             // unless this tar file lacks a pre-compiled segment graph
             // in which case we'll always generate a new tar file with
             // the graph to speed up future garbage collection runs.
+            // offline compaction will ignore the savings threshold and create a
+            // new tar file on each run.
             log.debug("Not enough space savings. ({}/{}). Skipping clean up of {}",
                     access.length() - size, access.length(), name);
             return this;