Index: src/shell.c
==================================================================
--- src/shell.c
+++ src/shell.c
@@ -522,11 +522,11 @@
     }
   }
 #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;
       if( nTrans>nLine ){
         zLine = realloc(zLine, nTrans);
@@ -4903,11 +4903,11 @@
   while( errCnt==0 || !bail_on_error || (in==0 && stdin_is_interactive) ){
     fflush(p->out);
     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 ){
       if( in!=0 ) break;
       seenInterrupt = 0;

Index: src/where.c
==================================================================
--- src/where.c
+++ src/where.c
@@ -3519,10 +3519,18 @@
       if( pOBExpr->op!=TK_COLUMN ) continue;
       if( pOBExpr->iTable!=iCur ) continue;
       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);
         if( !pColl ) pColl = db->pDfltColl;
         z1 = pColl->zName;

Index: test/limit2.test
==================================================================
--- test/limit2.test
+++ test/limit2.test
@@ -94,11 +94,22 @@
 } {2 2 2 12345 |}
 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 .}
 
 
 
 
 finish_test

Index: test/shell4.test
==================================================================
--- test/shell4.test
+++ test/shell4.test
@@ -16,10 +16,11 @@
 
 # Test plan:
 #
 #   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
 set CLI [test_find_cli]
 db close
@@ -122,7 +123,19 @@
 do_test shell4-2.5 {
   catchcmd ":memory:" "CREATE TABLE t1(x);\n.trace stdout\nSELECT * FROM t1;"
 } {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