Taken from http://sources.endlessm.com/debian/pool/core/n/ntfs-3g/ntfs-3g_2014.2.15AR.2-1%2bdeb8u2endless4.debian.tar.xz for ease of linking.

endless-ntfsextents-merged-runs.patch

ntfsextents: fix incorrect handling of merged runs

After the filesystem is defragmented, ntfsextents produced suspicious output
like the following:

...
47934664704 292540416
47934664704 930017280
47934664704 2045247488
...

where a section of the disk repeats. This corresponds to the LCN_RL_NOT_MAPPED
case: it seems that a series of contiguous extents can be represented by more
than one runlist element referencing the same base VCN.  The correct mapping
for the example above is:

...
47934664704 292540416
48227205120 637476864
48864681984 1115230208
...

which is what we produce with this patch, which is derived from the
corresponding logic in ntfs_attr_pread_i().

The following equivalent, more aesthetically-pleasing output is not worth the
hassle to produce:

...
47934664704 2045247488
...

https://phabricator.endlessm.com/T13743
Index: ntfs-3g-2014.2.15AR.2/ntfsprogs/ntfsextents.c
===================================================================
--- ntfs-3g-2014.2.15AR.2.orig/ntfsprogs/ntfsextents.c
+++ ntfs-3g-2014.2.15AR.2/ntfsprogs/ntfsextents.c
@@ -42,7 +42,7 @@ int main(int argc, const char *argv[])
 	ntfs_inode *ni;
 	ntfs_attr *na = NULL;
 	runlist_element *rl;
-	s64 remaining;
+	s64 ofs, total, remaining;
 
 	ntfs_log_set_handler(ntfs_log_handler_stderr);
 
@@ -100,7 +100,8 @@ int main(int argc, const char *argv[])
 		goto out;
 	}
 
-	for (remaining = na->data_size; remaining; rl++) {
+	ofs = - (rl->vcn << vol->cluster_size_bits);
+	for (total = 0, remaining = na->data_size; remaining; rl++, ofs = 0) {
 		unsigned long data_size;
 
 		if (rl->lcn == LCN_RL_NOT_MAPPED) {
@@ -110,6 +111,8 @@ int main(int argc, const char *argv[])
 					ntfs_log_error("ERROR: Failed to find VCN #2\n");
 				goto out;
 			}
+			/* Needed for case when runs merged. */
+			ofs = total - (rl->vcn << vol->cluster_size_bits);
 		}
 		if (!rl->length) {
 			ntfs_log_error("ERROR: Zero run length\n");
@@ -123,8 +126,9 @@ int main(int argc, const char *argv[])
 			ntfs_log_error("ERROR: File has hole\n");
 			goto out;
 		}
-		data_size = min(remaining, rl->length << vol->cluster_size_bits);
-		printf("%ld %ld\n", rl->lcn << vol->cluster_size_bits, data_size);
+		data_size = min(remaining, (rl->length << vol->cluster_size_bits) - ofs);
+		printf("%ld %ld\n", (rl->lcn << vol->cluster_size_bits) + ofs, data_size);
+		total += data_size;
 		remaining -= data_size;
 	}