diff --git a/manifest b/manifest
index b6583d963c..d9dec4830b 100644
--- a/manifest
+++ b/manifest
@@ -1,5 +1,5 @@
-C Remove\sobsolete\svector-IN\stest\scases.\s\sFix\sa\sbad\stestcase()\smacro.
-D 2016-09-06T19:08:21.705
+C Merge\sfixes\sfrom\strunk.
+D 2016-09-07T13:12:13.158
 F Makefile.in cfd8fb987cd7a6af046daa87daa146d5aad0e088
 F Makefile.linux-gcc 7bc79876b875010e8c8f9502eb935ca92aa3c434
 F Makefile.msc 5017381e4853b1472e01d5bb926be1268eba429c
@@ -386,7 +386,7 @@ F src/random.c ba2679f80ec82c4190062d756f22d0c358180696
 F src/resolve.c 24f40fd0c3475821d1ad762a3f2c3455cc839b42
 F src/rowset.c 7b7e7e479212e65b723bf40128c7b36dc5afdfac
 F src/select.c 244f9cc5e4662987cd2ef5c22d1b7027560f3425
-F src/shell.c 79dda477be6c96eba6e952a934957ad36f87acc7
+F src/shell.c de7c7e98846cacbfbe062cbd98bca899dfb720e3
 F src/sqlite.h.in 4a030e254e204570444b34bf7d40fb4a5416089e
 F src/sqlite3.rc 5121c9e10c3964d5755191c80dd1180c122fc3a8
 F src/sqlite3ext.h 8648034aa702469afb553231677306cc6492a1ae
@@ -465,7 +465,7 @@ F src/vxworks.h d2988f4e5a61a4dfe82c6524dd3d6e4f2ce3cdb9
 F src/wal.c 02eeecc265f6ffd0597378f5d8ae9070b62a406a
 F src/wal.h 6dd221ed384afdc204bc61e25c23ef7fd5a511f2
 F src/walker.c 2d2cc7fb0f320f7f415215d7247f3c584141ac09
-F src/where.c 48d705e5196a0611a7be90698eade455ee238536
+F src/where.c edbd73a87ba2e186928e9bfc14348b1bbb2628c5
 F src/whereInt.h 14dd243e13b81cbb0a66063d38b70f93a7d6e613
 F src/wherecode.c b0d4febdd9de07ad68faadeacb30df9785f9b979
 F src/whereexpr.c e3db778ed205e982f31960896db71c50612ae009
@@ -890,7 +890,7 @@ F test/like.test 81632c437a947bf1f7130b19537da6a1a844806a
 F test/like2.test 3b2ee13149ba4a8a60b59756f4e5d345573852da
 F test/like3.test 3608a2042b6f922f900fbfd5d3ce4e7eca57f7c4
 F test/limit.test 0c99a27a87b14c646a9d583c7c89fd06c352663e
-F test/limit2.test 40e79f3d95f2077742aa5b7676f58c9af1735d83
+F test/limit2.test ac97b8d07060a0280162ba4159e4c0c765861127
 F test/loadext.test d077450695ddb5c1ea3ad7d48e5f5850fe732ad9
 F test/loadext2.test 0408380b57adca04004247179837a18e866a74f7
 F test/lock.test be4fe08118fb988fed741f429b7dd5d65e1c90db
@@ -1080,7 +1080,7 @@ F test/sharedlock.test 5ede3c37439067c43b0198f580fd374ebf15d304
 F test/shell1.test 65b10cd8a90cda9b5af9100a45689a57dcc01a31
 F test/shell2.test e242a9912f44f4c23c3d1d802a83e934e84c853b
 F test/shell3.test da513d522ef6f01cee8475dcf8332bff8982b3dd
-F test/shell4.test 69995ee1cc278eb149aa8746ce1f935f4eaf98b9
+F test/shell4.test 89ad573879a745974ff2df20ff97c5d6ffffbd5d
 F test/shell5.test 50a732c1c2158b1cd62cf53975ce1ea7ce6b9dc9
 F test/shortread1.test bb591ef20f0fd9ed26d0d12e80eee6d7ac8897a3
 F test/show_speedtest1_rtree.tcl 32e6c5f073d7426148a6936a0408f4b5b169aba5
@@ -1522,7 +1522,7 @@ F vsixtest/vsixtest.tcl 6a9a6ab600c25a91a7acc6293828957a386a8a93
 F vsixtest/vsixtest.vcxproj.data 2ed517e100c66dc455b492e1a33350c1b20fbcdc
 F vsixtest/vsixtest.vcxproj.filters 37e51ffedcdb064aad6ff33b6148725226cd608e
 F vsixtest/vsixtest_TemporaryKey.pfx e5b1b036facdb453873e7084e1cae9102ccc67a0
-P 8329ac6f8d1edcc19c3e0559abe9a8011dbe1497
-R c63acfebc9bb94150dde03620f804079
+P ab3f8f193a7ec36018bf26c9231a1a6a58b6a523 d8451fe84d09db6ec7e1bd5f0708ea1b5e85f3d6
+R 9be49f79015d1d1f29328535fe4e7eb6
 U drh
-Z 4492b1886315f856574968e31e230cb0
+Z 2891e6cf4d042c296a4853701a08d60f
diff --git a/manifest.uuid b/manifest.uuid
index 130764cfa2..c5b7f13bc8 100644
--- a/manifest.uuid
+++ b/manifest.uuid
@@ -1 +1 @@
-ab3f8f193a7ec36018bf26c9231a1a6a58b6a523
\ No newline at end of file
+193f036c87857bd77577ceb462af5034c7cc77da
\ No newline at end of file
diff --git a/src/shell.c b/src/shell.c
index 18c6ef7197..21cba66b1c 100644
--- a/src/shell.c
+++ b/src/shell.c
@@ -524,7 +524,7 @@ static char *local_getline(char *zLine, FILE *in){
 #if defined(_WIN32) || defined(WIN32)
   /* For interactive input on Windows systems, translate the
   ** multi-byte characterset characters into UTF-8. */
-  if( stdin_is_interactive ){
+  if( stdin_is_interactive && in==stdin ){
     char *zTrans = sqlite3_win32_mbcs_to_utf8_v2(zLine, 0);
     if( zTrans ){
       int nTrans = strlen30(zTrans)+1;
@@ -4905,7 +4905,7 @@ static int process_input(ShellState *p, FILE *in){
     zLine = one_input_line(in, zLine, nSql>0);
     if( zLine==0 ){
       /* End of input */
-      if( stdin_is_interactive ) printf("\n");
+      if( in==0 && stdin_is_interactive ) printf("\n");
       break;
     }
     if( seenInterrupt ){
diff --git a/src/where.c b/src/where.c
index f60d5be6da..1785107244 100644
--- a/src/where.c
+++ b/src/where.c
@@ -3521,6 +3521,14 @@ static i8 wherePathSatisfiesOrderBy(
       pTerm = sqlite3WhereFindTerm(&pWInfo->sWC, iCur, pOBExpr->iColumn,
                        ~ready, eqOpMask, 0);
       if( pTerm==0 ) continue;
+      if( pTerm->eOperator==WO_IN ){
+        /* IN terms are only valid for sorting in the ORDER BY LIMIT 
+        ** optimization, and then only if they are actually used
+        ** by the query plan */
+        assert( wctrlFlags & WHERE_ORDERBY_LIMIT );
+        for(j=0; j<pLoop->nLTerm && pTerm!=pLoop->aLTerm[j]; j++){}
+        if( j>=pLoop->nLTerm ) continue;
+      }
       if( (pTerm->eOperator&(WO_EQ|WO_IS))!=0 && pOBExpr->iColumn>=0 ){
         const char *z1, *z2;
         pColl = sqlite3ExprCollSeq(pWInfo->pParse, pOrderBy->a[i].pExpr);
diff --git a/test/limit2.test b/test/limit2.test
index fb4c89644f..0f82ab8d55 100644
--- a/test/limit2.test
+++ b/test/limit2.test
@@ -96,7 +96,18 @@ do_execsql_test limit2-210 {
   SELECT *, '|' FROM t200 LEFT JOIN t201 ON x=b ORDER BY y LIMIT 3;
 } {1 1 {} {} | 3 3 {} {} | 4 4 {} {} |}
 
-
+# Bug in the ORDER BY LIMIT optimization reported on 2016-09-06.
+# Ticket https://www.sqlite.org/src/info/559733b09e96
+#
+do_execsql_test limit2-300 {
+  CREATE TABLE t300(a,b,c);
+  CREATE INDEX t300x ON t300(a,b,c);
+  INSERT INTO t300 VALUES(0,1,99),(0,1,0),(0,0,0);
+  SELECT *,'.' FROM t300 WHERE a=0 AND (c=0 OR c=99) ORDER BY c DESC;
+} {0 1 99 . 0 0 0 . 0 1 0 .}
+do_execsql_test limit2-310 {
+  SELECT *,'.' FROM t300 WHERE a=0 AND (c=0 OR c=99) ORDER BY c DESC LIMIT 1;
+} {0 1 99 .}
 
 
 
diff --git a/test/shell4.test b/test/shell4.test
index 3e4ae55816..88e5e69a28 100644
--- a/test/shell4.test
+++ b/test/shell4.test
@@ -18,6 +18,7 @@
 #
 #   shell4-1.*: Basic tests specific to the "stats" command.
 #   shell4-2.*: Basic tests for ".trace"
+#   shell4-3.*: The ".read" command takes the shell out of interactive mode
 #
 set testdir [file dirname $argv0]
 source $testdir/tester.tcl
@@ -124,5 +125,17 @@ do_test shell4-2.5 {
 } {0 {SELECT * FROM t1;}}
 }
 
+do_test shell4-3.1 {
+  set fd [open t1.txt wb]
+  puts $fd "SELECT 'squirrel';"
+  close $fd
+  exec $::CLI :memory: --interactive ".read t1.txt"
+} {squirrel}
+do_test shell4-3.2 {
+  set fd [open t1.txt wb]
+  puts $fd "SELECT 'pound: \302\243';"
+  close $fd
+  exec $::CLI :memory: --interactive ".read t1.txt"
+} {pound: £}
 
 finish_test