diff --git a/manifest b/manifest
index 8b4409d2ff..98dcf120d9 100644
--- a/manifest
+++ b/manifest
@@ -1,5 +1,5 @@
-C Fix\ssome\sproblems\swith\smulti-column\sIN(SELECT...)\sprocessing.
-D 2016-07-27T19:33:04.107
+C Merge\slatest\strunk\schanges\sinto\sthis\sbranch.
+D 2016-07-28T13:59:21.728
 F Makefile.in 6c20d44f72d4564f11652b26291a214c8367e5db
 F Makefile.linux-gcc 7bc79876b875010e8c8f9502eb935ca92aa3c434
 F Makefile.msc d66d0395c38571aab3804f8db0fa20707ae4609a
@@ -337,7 +337,7 @@ F src/ctime.c 61949e83c4c36e37195a8398ebc752780b534d95
 F src/date.c 1cc9fb516ec9932c6fd4d2a0d2f8bc4480145c39
 F src/dbstat.c 4f6f7f52b49beb9636ffbd517cfe44a402ba4ad0
 F src/delete.c 4aba4214a377ce8ddde2d2e609777bcc8235200f
-F src/expr.c bee29fbb017db26ad1189d35b2a7fe6ff8da3722
+F src/expr.c 82bc40bb27bc68b45303b560ab14eb16e39786a7
 F src/fault.c 160a0c015b6c2629d3899ed2daf63d75754a32bb
 F src/fkey.c bc4145347595b7770f9a598cff1c848302cf5413
 F src/func.c 61a4114cf7004f10c542cfabbab9f2bcb9033045
@@ -388,7 +388,7 @@ F src/shell.c 9351fc6de11e1d908648c0a92d85627138e3dee5
 F src/sqlite.h.in c6e68a4a47610631822a4f8f83a44c9f75339331
 F src/sqlite3.rc 5121c9e10c3964d5755191c80dd1180c122fc3a8
 F src/sqlite3ext.h 46f300b6e300e0fa916d7d58c44b53415b8471a9
-F src/sqliteInt.h 9a6af8787f03f54ce02ff88bd45f89bb600c3a4c
+F src/sqliteInt.h 65cf752e1a62cedb2430ecc0547a09833ea13616
 F src/sqliteLimit.h c0373387c287c8d0932510b5547ecde31b5da247
 F src/status.c 5b18f9526900f61189ab0b83f1ef41d9f871a2ab
 F src/table.c 5226df15ab9179b9ed558d89575ea0ce37b03fc9
@@ -463,7 +463,7 @@ F src/vxworks.h d2988f4e5a61a4dfe82c6524dd3d6e4f2ce3cdb9
 F src/wal.c 02eeecc265f6ffd0597378f5d8ae9070b62a406a
 F src/wal.h 6dd221ed384afdc204bc61e25c23ef7fd5a511f2
 F src/walker.c 0f142b5bd3ed2041fc52d773880748b212e63354
-F src/where.c 0b370db8ce08fac93a098f27eaf425d2269be376
+F src/where.c df58d6ad7878a08aa96c652ccbc6d0949f8fa472
 F src/whereInt.h 14dd243e13b81cbb0a66063d38b70f93a7d6e613
 F src/wherecode.c 3aff7683566af3428f865904aafa7efb1fbd8701
 F src/whereexpr.c b896f8ff6a53cbd3daaee84ec33e39098762bb46
@@ -845,6 +845,7 @@ F test/index4.test ab92e736d5946840236cd61ac3191f91a7856bf6
 F test/index5.test 8621491915800ec274609e42e02a97d67e9b13e7
 F test/index6.test 43b4e29258b978fcdab84fc61df4f5212119dd09
 F test/index7.test 9c6765a74fc3fcde7aebc5b3bd40d98df14a527c
+F test/index8.test bc2e3db70e8e62459aaa1bd7e4a9b39664f8f9d7
 F test/indexedby.test 9c4cd331224e57f79fbf411ae245e6272d415985
 F test/indexexpr1.test cb71b6586177b840e28110dd952178bb2bdfedc2
 F test/indexfault.test 31d4ab9a7d2f6e9616933eb079722362a883eb1d
@@ -984,7 +985,7 @@ F test/pagerfault2.test caf4c7facb914fd3b03a17b31ae2b180c8d6ca1f
 F test/pagerfault3.test 1003fcda009bf48a8e22a516e193b6ef0dd1bbd8
 F test/pageropt.test 84e4cc5cbca285357f7906e99b21be4f2bf5abc0
 F test/pagesize.test 5769fc62d8c890a83a503f67d47508dfdc543305
-F test/parser1.test 222b5cbf3e2e659fec1bf7d723488c8b9c94f1d0
+F test/parser1.test 391b9bf9a229547a129c61ac345ed1a6f5eb1854
 F test/pcache.test c8acbedd3b6fd0f9a7ca887a83b11d24a007972b
 F test/pcache2.test af7f3deb1a819f77a6d0d81534e97d1cf62cd442
 F test/percentile.test 4243af26b8f3f4555abe166f723715a1f74c77ff
@@ -1029,7 +1030,7 @@ F test/savepoint5.test 0735db177e0ebbaedc39812c8d065075d563c4fd
 F test/savepoint6.test f41279c5e137139fa5c21485773332c7adb98cd7
 F test/savepoint7.test cde525ea3075283eb950cdcdefe23ead4f700daa
 F test/savepointfault.test f044eac64b59f09746c7020ee261734de82bf9b2
-F test/scanstatus.test 5253c219e331318a437f436268e0e82345700285
+F test/scanstatus.test 030acbbdcea6a3fc676fee99edc84f6f16c0cf92
 F test/schema.test 8f7999be894260f151adf15c2c7540f1c6d6a481
 F test/schema2.test 906408621ea881fdb496d878b1822572a34e32c5
 F test/schema3.test 1bc1008e1f8cb5654b248c55f27249366eb7ed38
@@ -1510,7 +1511,7 @@ F vsixtest/vsixtest.tcl 6a9a6ab600c25a91a7acc6293828957a386a8a93
 F vsixtest/vsixtest.vcxproj.data 2ed517e100c66dc455b492e1a33350c1b20fbcdc
 F vsixtest/vsixtest.vcxproj.filters 37e51ffedcdb064aad6ff33b6148725226cd608e
 F vsixtest/vsixtest_TemporaryKey.pfx e5b1b036facdb453873e7084e1cae9102ccc67a0
-P d4f3d52c5a11fc7ad7e8cad76361edbcef13a12f 4d59df02d3713b3e3804e1a88e676749b2794286
-R 1d3755c62e27d021f9887ac09a170360
+P 719a3b2035a335ca8b9704646b1d641011e3ea0e 6feff15cae8f0427be790355841d49c479c1c586
+R 3c287799720eaa100d938a8b5fd4645d
 U dan
-Z 2549ddc5292b60c5848a8cde952880f9
+Z 3b75e2ba5b9150b77f0261ae152b7ba4
diff --git a/manifest.uuid b/manifest.uuid
index 21c7478815..88af2bcaa6 100644
--- a/manifest.uuid
+++ b/manifest.uuid
@@ -1 +1 @@
-719a3b2035a335ca8b9704646b1d641011e3ea0e
\ No newline at end of file
+9685880f7baeb670739fdcf2d9df08e22abaa699
\ No newline at end of file
diff --git a/src/expr.c b/src/expr.c
index 3c95136c5c..26587309f2 100644
--- a/src/expr.c
+++ b/src/expr.c
@@ -4312,6 +4312,61 @@ int sqlite3ExprImpliesExpr(Expr *pE1, Expr *pE2, int iTab){
   return 0;
 }
 
+/*
+** An instance of the following structure is used by the tree walker
+** to determine if an expression can be evaluated by reference to the
+** index only, without having to do a search for the corresponding
+** table entry.  The IdxCover.pIdx field is the index.  IdxCover.iCur
+** is the cursor for the table.
+*/
+struct IdxCover {
+  Index *pIdx;     /* The index to be tested for coverage */
+  int iCur;        /* Cursor number for the table corresponding to the index */
+};
+
+/*
+** Check to see if there are references to columns in table 
+** pWalker->u.pIdxCover->iCur can be satisfied using the index
+** pWalker->u.pIdxCover->pIdx.
+*/
+static int exprIdxCover(Walker *pWalker, Expr *pExpr){
+  if( pExpr->op==TK_COLUMN
+   && pExpr->iTable==pWalker->u.pIdxCover->iCur
+   && sqlite3ColumnOfIndex(pWalker->u.pIdxCover->pIdx, pExpr->iColumn)<0
+  ){
+    pWalker->eCode = 1;
+    return WRC_Abort;
+  }
+  return WRC_Continue;
+}
+
+/*
+** Determine if an index pIdx on table with cursor iCur contains will
+** the expression pExpr.  Return true if the index does cover the
+** expression and false if the pExpr expression references table columns
+** that are not found in the index pIdx.
+**
+** An index covering an expression means that the expression can be
+** evaluated using only the index and without having to lookup the
+** corresponding table entry.
+*/
+int sqlite3ExprCoveredByIndex(
+  Expr *pExpr,        /* The index to be tested */
+  int iCur,           /* The cursor number for the corresponding table */
+  Index *pIdx         /* The index that might be used for coverage */
+){
+  Walker w;
+  struct IdxCover xcov;
+  memset(&w, 0, sizeof(w));
+  xcov.iCur = iCur;
+  xcov.pIdx = pIdx;
+  w.xExprCallback = exprIdxCover;
+  w.u.pIdxCover = &xcov;
+  sqlite3WalkExpr(&w, pExpr);
+  return !w.eCode;
+}
+
+
 /*
 ** An instance of the following structure is used by the tree walker
 ** to count references to table columns in the arguments of an 
diff --git a/src/sqliteInt.h b/src/sqliteInt.h
index 7219732bc3..ea41e65755 100644
--- a/src/sqliteInt.h
+++ b/src/sqliteInt.h
@@ -3258,6 +3258,7 @@ struct Walker {
     struct SrcCount *pSrcCount;                /* Counting column references */
     struct CCurHint *pCCurHint;                /* Used by codeCursorHint() */
     int *aiCol;                                /* array of column indexes */
+    struct IdxCover *pIdxCover;                /* Check for index coverage */
   } u;
 };
 
@@ -3701,6 +3702,7 @@ int sqlite3ExprListCompare(ExprList*, ExprList*, int);
 int sqlite3ExprImpliesExpr(Expr*, Expr*, int);
 void sqlite3ExprAnalyzeAggregates(NameContext*, Expr*);
 void sqlite3ExprAnalyzeAggList(NameContext*,ExprList*);
+int sqlite3ExprCoveredByIndex(Expr*, int iCur, Index *pIdx);
 int sqlite3FunctionUsesThisSrc(Expr*, SrcList*);
 Vdbe *sqlite3GetVdbe(Parse*);
 #ifndef SQLITE_OMIT_BUILTIN_TEST
diff --git a/src/where.c b/src/where.c
index 6c039c6b7c..fdf0be7358 100644
--- a/src/where.c
+++ b/src/where.c
@@ -2539,11 +2539,11 @@ static int whereLoopAddBtreeIndex(
     pNew->nSkip++;
     pNew->aLTerm[pNew->nLTerm++] = 0;
     pNew->wsFlags |= WHERE_SKIPSCAN;
-    nIter = pProbe->aiRowLogEst[saved_nEq] - pProbe->aiRowLogEst[saved_nEq+1];
+    nIter = pProbe->aiRowLogEst[saved_nEq]+1 - pProbe->aiRowLogEst[saved_nEq+1];
     pNew->nOut -= nIter;
     /* TUNING:  Because uncertainties in the estimates for skip-scan queries,
     ** add a 1.375 fudge factor to make skip-scan slightly less likely. */
-    nIter += 5;
+    nIter += 4;
     whereLoopAddBtreeIndex(pBuilder, pSrc, pProbe, nIter + nInMul);
     pNew->nOut = saved_nOut;
     pNew->u.btree.nEq = saved_nEq;
@@ -2838,11 +2838,34 @@ static int whereLoopAddBtree(
 
         /* The cost of visiting the index rows is N*K, where K is
         ** between 1.1 and 3.0, depending on the relative sizes of the
-        ** index and table rows. If this is a non-covering index scan,
-        ** also add the cost of visiting table rows (N*3.0).  */
+        ** index and table rows. */
         pNew->rRun = rSize + 1 + (15*pProbe->szIdxRow)/pTab->szTabRow;
         if( m!=0 ){
-          pNew->rRun = sqlite3LogEstAdd(pNew->rRun, rSize+16);
+          /* If this is a non-covering index scan, add in the cost of
+          ** doing table lookups.  The cost will be 3x the number of
+          ** lookups.  Take into account WHERE clause terms that can be
+          ** satisfied using just the index, and that do not require a
+          ** table lookup. */
+          LogEst nLookup = rSize + 16;  /* Base cost:  N*3 */
+          int ii;
+          int iCur = pSrc->iCursor;
+          WhereClause *pWC = &pWInfo->sWC;
+          for(ii=0; ii<pWC->nTerm; ii++){
+            WhereTerm *pTerm = &pWC->a[ii];
+            if( !sqlite3ExprCoveredByIndex(pTerm->pExpr, iCur, pProbe) ){
+              break;
+            }
+            /* pTerm can be evaluated using just the index.  So reduce
+            ** the expected number of table lookups accordingly */
+            if( pTerm->truthProb<=0 ){
+              nLookup += pTerm->truthProb;
+            }else{
+              nLookup--;
+              if( pTerm->eOperator & (WO_EQ|WO_IS) ) nLookup -= 19;
+            }
+          }
+          
+          pNew->rRun = sqlite3LogEstAdd(pNew->rRun, nLookup);
         }
         ApplyCostMultiplier(pNew->rRun, pTab->costMult);
         whereLoopOutputAdjust(pWC, pNew, rSize);
diff --git a/test/index8.test b/test/index8.test
new file mode 100644
index 0000000000..bb58228527
--- /dev/null
+++ b/test/index8.test
@@ -0,0 +1,60 @@
+# 2016-07-27
+#
+# The author disclaims copyright to this source code.  In place of
+# a legal notice, here is a blessing:
+#
+#    May you do good and not evil.
+#    May you find forgiveness for yourself and forgive others.
+#    May you share freely, never taking more than you give.
+#
+#***********************************************************************
+#
+# Test cases for ORDER BY and LIMIT on an index scan.
+#
+
+
+set testdir [file dirname $argv0]
+source $testdir/tester.tcl
+
+# Performance regression reported at
+# http://www.mail-archive.com/sqlite-users@mailinglists.sqlite.org/msg98615.html
+#
+# Caused by the ORDER BY LIMIT optionation for check-in
+# https://sqlite.org/src/info/bf46179d44843769
+#
+# Fixed on approximately 2016-07-27 by changes that compute a better score
+# for index scans by taking into account WHERE clause constraints that can
+# be handled by the index and do not require a table lookup.
+#
+do_execsql_test 1.0 {
+  CREATE TABLE t1(a,b,c,d);
+  WITH RECURSIVE c(x) AS (VALUES(0) UNION ALL SELECT x+1 FROM c WHERE x<100)
+  INSERT INTO t1(a,b,c,d)
+     SELECT x/10, x%10, x%19, x FROM c;
+  CREATE INDEX t1abc ON t1(a,b,c);
+  SELECT * FROM t1 WHERE c=4 ORDER BY a, b LIMIT 2;
+} {0 4 4 4 2 3 4 23}
+
+# Prior to the fix, the following EQP would show a table scan and a sort
+# rather than an index scan.
+#
+do_execsql_test 1.0eqp {
+  EXPLAIN QUERY PLAN
+  SELECT * FROM t1 WHERE c=4 ORDER BY a, b LIMIT 2;
+} {/SCAN TABLE t1 USING INDEX t1abc/}
+
+# If we change the index so that it no longer covers the WHERE clause,
+# then we should (correctly) revert to using a table scan.
+#
+do_execsql_test 1.1 {
+  DROP INDEX t1abc;
+  CREATE INDEX t1abd ON t1(a,b,d);
+  SELECT * FROM t1 WHERE c=4 ORDER BY a, b LIMIT 2;
+} {0 4 4 4 2 3 4 23}
+do_execsql_test 1.1eqp {
+  EXPLAIN QUERY PLAN
+  SELECT * FROM t1 WHERE c=4 ORDER BY a, b LIMIT 2;
+} {~/USING INDEX/}
+
+
+finish_test
diff --git a/test/parser1.test b/test/parser1.test
index 78c1a40c63..c708dded1f 100644
--- a/test/parser1.test
+++ b/test/parser1.test
@@ -76,4 +76,27 @@ do_catchsql_test parser1-2.2 {
   SELECT x FROM c;
 } {1 {syntax error after column name "x"}}
 
+# Verify that the comma between multiple table constraints is
+# optional.
+#
+# The missing comma is technically a syntax error.  But we have to support
+# it because there might be legacy databases that omit the commas in their
+# sqlite_master tables.
+#
+do_execsql_test parser1-3.1 {
+  CREATE TABLE t300(id INTEGER PRIMARY KEY);
+  CREATE TABLE t301(
+    id INTEGER PRIMARY KEY,
+    c1 INTEGER NOT NULL,
+    c2 INTEGER NOT NULL,
+    c3 BOOLEAN NOT NULL DEFAULT 0,
+    FOREIGN KEY(c1) REFERENCES t300(id) ON DELETE CASCADE ON UPDATE RESTRICT
+        /* no comma */
+    FOREIGN KEY(c2) REFERENCES t300(id) ON DELETE CASCADE ON UPDATE RESTRICT
+        /* no comma */
+    UNIQUE(c1, c2)
+  );
+  PRAGMA foreign_key_list(t301);
+} {0 0 t300 c2 id RESTRICT CASCADE NONE 1 0 t300 c1 id RESTRICT CASCADE NONE}
+
 finish_test
diff --git a/test/scanstatus.test b/test/scanstatus.test
index ed24d97437..48365a8794 100644
--- a/test/scanstatus.test
+++ b/test/scanstatus.test
@@ -333,7 +333,7 @@ do_execsql_test 5.3.2 {
   SELECT count(*) FROM t2 WHERE y = 'j';
 } {19}
 do_scanstatus_test 5.3.3 { 
-  nLoop 1 nVisit 19 nEst 56.0 zName t2xy zExplain
+  nLoop 1 nVisit 19 nEst 52.0 zName t2xy zExplain
   {SEARCH TABLE t2 USING COVERING INDEX t2xy (ANY(x) AND y=?)}
 }
 
@@ -349,7 +349,7 @@ do_execsql_test 5.4.2 {
 do_scanstatus_test 5.4.3 { 
   nLoop 1 nVisit 10 nEst 10.0 zName t1bc 
   zExplain {SCAN TABLE t1 USING COVERING INDEX t1bc}
-  nLoop 10 nVisit 200 nEst 56.0 zName t2xy 
+  nLoop 10 nVisit 200 nEst 52.0 zName t2xy 
   zExplain {SEARCH TABLE t2 USING COVERING INDEX t2xy (ANY(x) AND y=?)}
 }