diff --git a/ext/rbu/rbudiff.test b/ext/rbu/rbudiff.test
index 0863f6e807..fa8de319dd 100644
--- a/ext/rbu/rbudiff.test
+++ b/ext/rbu/rbudiff.test
@@ -25,6 +25,10 @@ proc get_rbudiff_sql {db1 db2} {
   exec $::PROG --rbu $db1 $db2
 }
 
+proc get_vtab_rbudiff_sql {db1 db2} {
+  exec $::PROG --vtab --rbu $db1 $db2
+}
+
 proc step_rbu {target rbu} {
   while 1 {
     sqlite3rbu rbu $target $rbu
@@ -44,6 +48,11 @@ proc apply_rbudiff {sql target} {
   step_rbu $target rbu.db
 }
 
+proc sqlesc {id} {
+  set ret "'[string map {' ''} $id]'"
+  set ret
+}
+
 # The only argument is the output of an [sqldiff -rbu] run. This command
 # tests that the contents of the rbu_count table is correct. An exception
 # is thrown if it is not.
@@ -54,7 +63,7 @@ proc test_rbucount {sql} {
   tmpdb eval {
     SELECT name FROM sqlite_master WHERE name LIKE 'data%' AND type='table'
   } {
-    set a [tmpdb eval "SELECT count(*) FROM $name"]
+    set a [tmpdb eval "SELECT count(*) FROM [sqlesc $name]"]
     set b [tmpdb eval {SELECT cnt FROM rbu_count WHERE tbl = $name}]
     if {$a != $b} { 
       tmpdb close
@@ -71,9 +80,11 @@ proc rbudiff_cksum {db1} {
   sqlite3 dbtmp $db1
   foreach tbl [dbtmp eval {SELECT name FROM sqlite_master WHERE type='table'}] {
     set cols [list]
-    dbtmp eval "PRAGMA table_info = $tbl" { lappend cols "quote( $name )" }
+    dbtmp eval "PRAGMA table_info = [sqlesc $tbl]" { 
+      lappend cols "quote( $name )" 
+    }
     append txt [dbtmp eval \
-      "SELECT [join $cols {||'.'||}] FROM $tbl ORDER BY 1"
+      "SELECT [join $cols {||'.'||}] FROM [sqlesc $tbl] ORDER BY 1"
     ]
   }
   dbtmp close
@@ -159,5 +170,57 @@ foreach {tn init mod} {
   do_test 1.$tn.5 { rbudiff_cksum test.db } [rbudiff_cksum test.db2]
 }
 
+#-------------------------------------------------------------------------
+# Test that if the --vtab switch is present, [sqldiff] handles virtual
+# table types fts[345] and rtree correctly.
+#
+ifcapable fts3&&fts5&&rtree {
+
+foreach {tn init mod} {
+  1 {
+    CREATE VIRTUAL TABLE t1 USING fts5(c);
+    INSERT INTO t1 VALUES('a b c');
+    INSERT INTO t1 VALUES('a b c');
+  } {
+    DELETE FROM t1 WHERE rowid = 1;
+    INSERT INTO t1 VALUES('a b c');
+  }
+
+  2 {
+    CREATE VIRTUAL TABLE "x y" USING 'rtree'(id, x1, x2);
+    INSERT INTO "x y" VALUES(1, 2, 3);
+    INSERT INTO "x y" VALUES(2, 4, 6);
+  } {
+    DELETE FROM "x y" WHERE rowid = 1;
+    INSERT INTO "x y" VALUES(3, 6, 9);
+  }
+
+  3 {
+    CREATE VIRTUAL TABLE 'x''y' USING fts3;
+    INSERT INTO 'x''y' VALUES('one two three');
+    INSERT INTO 'x''y' VALUES('four five six');
+  } {
+    DELETE FROM 'x''y' WHERE rowid = 1;
+    INSERT INTO 'x''y' VALUES('one two three');
+  }
+
+} {
+
+  forcedelete test.db test.db2
+  sqlite3 db test.db
+  db eval "$init"
+  sqlite3 db test.db2
+  db eval "$init ; $mod"
+  db close
+
+  do_test 2.$tn.1 {
+    set sql [get_vtab_rbudiff_sql test.db test.db2]
+    apply_rbudiff $sql test.db
+  } {SQLITE_DONE}
+  do_test 2.$tn.2 { rbudiff_cksum test.db } [rbudiff_cksum test.db2]
+}
+
+}
+
 finish_test
 
diff --git a/manifest b/manifest
index 5a9145709f..6ede4001aa 100644
--- a/manifest
+++ b/manifest
@@ -1,5 +1,5 @@
-C Fix\sthe\sbuild\sfor\s-DSQLITE_OMIT_VIRTUALTABLE
-D 2016-06-23T12:35:04.863
+C Update\sthe\ssqldiff\sutility\sso\sthat\sif\sthe\s--vtab\sswitch\sis\sspecified\s"rtree",\s"fts3",\s"fts4"\sand\s"fts5"\stables\sare\sdiff'd\sdirectly\sand\sthe\sunderlying\sreal\sdatabase\stables\signored.\sWithout\sthis\sswitch,\sall\svirtual\stables\sare\signored\sand\sthe\sdiff\sis\sperformed\son\sthe\sunderlying\sreal\stables.
+D 2016-06-23T16:48:35.249
 F Makefile.in f3f7d2060ce03af4584e711ef3a626ef0b1d6340
 F Makefile.linux-gcc 7bc79876b875010e8c8f9502eb935ca92aa3c434
 F Makefile.msc 50149765ef72f4e652b9a0f1f6462c4784bb9423
@@ -243,7 +243,7 @@ F ext/rbu/rbuB.test c25bc325b8072a766e56bb76c001866b405925c2
 F ext/rbu/rbuC.test efe47db508a0269b683cb2a1913a425ffd39a831
 F ext/rbu/rbu_common.tcl 3a4b916b6f5dca9c9da9a30863e272fe5ea4414f
 F ext/rbu/rbucrash.test 8d2ed5d4b05fef6c00c2a6b5f7ead71fa172a695
-F ext/rbu/rbudiff.test 2df0a8a7d998ecf81764c21eeda3cde5611c5091
+F ext/rbu/rbudiff.test 4c9f8df6f723f553781d3d117501b7e9d170a145
 F ext/rbu/rbufault.test cc0be8d5d392d98b0c2d6a51be377ea989250a89
 F ext/rbu/rbufault2.test 9a7f19edd6ea35c4c9f807d8a3db0a03a5670c06
 F ext/rbu/rbufault3.test 54a399888ac4af44c68f9f58afbed23149428bca
@@ -1469,7 +1469,7 @@ F tool/speedtest2.tcl ee2149167303ba8e95af97873c575c3e0fab58ff
 F tool/speedtest8.c 2902c46588c40b55661e471d7a86e4dd71a18224
 F tool/speedtest8inst1.c 7ce07da76b5e745783e703a834417d725b7d45fd
 F tool/split-sqlite3c.tcl d9be87f1c340285a3e081eb19b4a247981ed290c
-F tool/sqldiff.c ca315aca4e2d24233e8f2000edea5880c53d1875
+F tool/sqldiff.c 131e9c6e09d3d78e3c4ae8b5fd23451521723aac
 F tool/srcck1.c 4c39bdfa9a92edd20233ee720df84dbeb2417602
 F tool/stack_usage.tcl f8e71b92cdb099a147dad572375595eae55eca43
 F tool/symbols-mingw.sh 4dbcea7e74768305384c9fd2ed2b41bbf9f0414d
@@ -1502,7 +1502,8 @@ F vsixtest/vsixtest.tcl 6a9a6ab600c25a91a7acc6293828957a386a8a93
 F vsixtest/vsixtest.vcxproj.data 2ed517e100c66dc455b492e1a33350c1b20fbcdc
 F vsixtest/vsixtest.vcxproj.filters 37e51ffedcdb064aad6ff33b6148725226cd608e
 F vsixtest/vsixtest_TemporaryKey.pfx e5b1b036facdb453873e7084e1cae9102ccc67a0
-P 913e595615e2ef40fb431f6e7678f6fc8439782e
-R b96a3531b275feb80cf3ff7b27074eda
-U drh
-Z 55a9839fb9d4bac563e41eaf1345cb2c
+P 911131424857430d46784b167399ecf192584ca2 5d0a9d4c45730e47576bc77373fa7075a74051a5
+R 208a102d85ab541408c6c49f684969ef
+T +closed 5d0a9d4c45730e47576bc77373fa7075a74051a5
+U dan
+Z c85e872c7e55cfaaf069baf7060cb813
diff --git a/manifest.uuid b/manifest.uuid
index 993a909ccc..e7770916f2 100644
--- a/manifest.uuid
+++ b/manifest.uuid
@@ -1 +1 @@
-911131424857430d46784b167399ecf192584ca2
\ No newline at end of file
+b8671e9434180878cfe15d70b793fdee69aabccf
\ No newline at end of file
diff --git a/tool/sqldiff.c b/tool/sqldiff.c
index 319acafdbd..4a5389c603 100644
--- a/tool/sqldiff.c
+++ b/tool/sqldiff.c
@@ -33,6 +33,7 @@ struct GlobalVars {
   const char *zArgv0;       /* Name of program */
   int bSchemaOnly;          /* Only show schema differences */
   int bSchemaPK;            /* Use the schema-defined PK, not the true PK */
+  int bHandleVtab;          /* Handle fts3, fts4, fts5 and rtree vtabs */
   unsigned fDebug;          /* Debug flags */
   sqlite3 *db;              /* The database connection */
 } g;
@@ -1735,6 +1736,144 @@ end_changeset_one_table:
   sqlite3_free(zId);
 }
 
+/*
+** Extract the next SQL keyword or quoted string from buffer zIn and copy it
+** (or a prefix of it if it will not fit) into buffer zBuf, size nBuf bytes.
+** Return a pointer to the character within zIn immediately following 
+** the token or quoted string just extracted.
+*/
+const char *gobble_token(const char *zIn, char *zBuf, int nBuf){
+  const char *p = zIn;
+  char *pOut = zBuf;
+  char *pEnd = &pOut[nBuf-1];
+  char q = 0;                     /* quote character, if any */
+
+  if( p==0 ) return 0;
+  while( *p==' ' ) p++;
+  switch( *p ){
+    case '"': q = '"'; break;
+    case '\'': q = '\''; break;
+    case '`': q = '`'; break;
+    case '[': q = ']'; break;
+  }
+
+  if( q ){
+    p++;
+    while( *p && pOut<pEnd ){
+      if( *p==q ){
+        p++;
+        if( *p!=q ) break;
+      }
+      if( pOut<pEnd ) *pOut++ = *p;
+      p++;
+    }
+  }else{
+    while( *p && *p!=' ' && *p!='(' ){
+      if( pOut<pEnd ) *pOut++ = *p;
+      p++;
+    }
+  }
+
+  *pOut = '\0';
+  return p;
+}
+
+/*
+** This function is the implementation of SQL scalar function "module_name":
+**
+**   module_name(SQL)
+**
+** The only argument should be an SQL statement of the type that may appear
+** in the sqlite_master table. If the statement is a "CREATE VIRTUAL TABLE"
+** statement, then the value returned is the name of the module that it
+** uses. Otherwise, if the statement is not a CVT, NULL is returned.
+*/
+static void module_name_func(
+  sqlite3_context *pCtx, 
+  int nVal, sqlite3_value **apVal
+){
+  const char *zSql;
+  char zToken[32];
+
+  assert( nVal==1 );
+  zSql = (const char*)sqlite3_value_text(apVal[0]);
+
+  zSql = gobble_token(zSql, zToken, sizeof(zToken));
+  if( zSql==0 || sqlite3_stricmp(zToken, "create") ) return;
+  zSql = gobble_token(zSql, zToken, sizeof(zToken));
+  if( zSql==0 || sqlite3_stricmp(zToken, "virtual") ) return;
+  zSql = gobble_token(zSql, zToken, sizeof(zToken));
+  if( zSql==0 || sqlite3_stricmp(zToken, "table") ) return;
+  zSql = gobble_token(zSql, zToken, sizeof(zToken));
+  if( zSql==0 ) return;
+  zSql = gobble_token(zSql, zToken, sizeof(zToken));
+  if( zSql==0 || sqlite3_stricmp(zToken, "using") ) return;
+  zSql = gobble_token(zSql, zToken, sizeof(zToken));
+  
+  sqlite3_result_text(pCtx, zToken, -1, SQLITE_TRANSIENT);
+}
+
+/*
+** Return the text of an SQL statement that itself returns the list of
+** tables to process within the database.
+*/
+const char *all_tables_sql(){
+  if( g.bHandleVtab ){
+    int rc;
+  
+    rc = sqlite3_exec(g.db, 
+        "CREATE TEMP TABLE tblmap(module, postfix);"
+        "INSERT INTO temp.tblmap VALUES"
+        "('fts3', '_content'), ('fts3', '_segments'), ('fts3', '_segdir'),"
+  
+        "('fts4', '_content'), ('fts4', '_segments'), ('fts4', '_segdir'),"
+        "('fts4', '_docsize'), ('fts4', '_stat'),"
+  
+        "('fts5', '_data'), ('fts5', '_idx'), ('fts5', '_content'),"
+        "('fts5', '_docsize'), ('fts5', '_config'),"
+  
+        "('rtree', '_node'), ('rtree', '_rowid'), ('rtree', '_parent');"
+        , 0, 0, 0
+    );
+    assert( rc==SQLITE_OK );
+  
+    rc = sqlite3_create_function(
+        g.db, "module_name", 1, SQLITE_UTF8, 0, module_name_func, 0, 0
+    );
+    assert( rc==SQLITE_OK );
+  
+    return 
+      "SELECT name FROM main.sqlite_master\n"
+      " WHERE type='table' AND (\n"
+      "    module_name(sql) IS NULL OR \n"
+      "    module_name(sql) IN (SELECT module FROM temp.tblmap)\n"
+      " ) AND name NOT IN (\n"
+      "  SELECT a.name || b.postfix \n"
+        "FROM main.sqlite_master AS a, temp.tblmap AS b \n"
+        "WHERE module_name(a.sql) = b.module\n" 
+      " )\n"
+      "UNION \n"
+      "SELECT name FROM aux.sqlite_master\n"
+      " WHERE type='table' AND (\n"
+      "    module_name(sql) IS NULL OR \n"
+      "    module_name(sql) IN (SELECT module FROM temp.tblmap)\n"
+      " ) AND name NOT IN (\n"
+      "  SELECT a.name || b.postfix \n"
+        "FROM aux.sqlite_master AS a, temp.tblmap AS b \n"
+        "WHERE module_name(a.sql) = b.module\n" 
+      " )\n"
+      " ORDER BY name";
+  }else{
+    return
+      "SELECT name FROM main.sqlite_master\n"
+      " WHERE type='table' AND sql NOT LIKE 'CREATE VIRTUAL%%'\n"
+      " UNION\n"
+      "SELECT name FROM aux.sqlite_master\n"
+      " WHERE type='table' AND sql NOT LIKE 'CREATE VIRTUAL%%'\n"
+      " ORDER BY name";
+  }
+}
+
 /*
 ** Print sketchy documentation for this utility program
 */
@@ -1751,6 +1890,7 @@ static void showHelp(void){
 "  --summary             Show only a summary of the differences\n"
 "  --table TAB           Show only differences in table TAB\n"
 "  --transaction         Show SQL output inside a transaction\n"
+"  --vtab                Handle fts3, fts4, fts5 and rtree tables\n"
   );
 }
 
@@ -1821,6 +1961,9 @@ int main(int argc, char **argv){
       if( strcmp(z,"transaction")==0 ){
         useTransaction = 1;
       }else
+      if( strcmp(z,"vtab")==0 ){
+        g.bHandleVtab = 1;
+      }else
       {
         cmdlineError("unknown option: %s", argv[i]);
       }
@@ -1875,14 +2018,7 @@ int main(int argc, char **argv){
     xDiff(zTab, out);
   }else{
     /* Handle tables one by one */
-    pStmt = db_prepare(
-      "SELECT name FROM main.sqlite_master\n"
-      " WHERE type='table' AND sql NOT LIKE 'CREATE VIRTUAL%%'\n"
-      " UNION\n"
-      "SELECT name FROM aux.sqlite_master\n"
-      " WHERE type='table' AND sql NOT LIKE 'CREATE VIRTUAL%%'\n"
-      " ORDER BY name"
-    );
+    pStmt = db_prepare( all_tables_sql() );
     while( SQLITE_ROW==sqlite3_step(pStmt) ){
       xDiff((const char*)sqlite3_column_text(pStmt,0), out);
     }