Index: src/where.c
==================================================================
--- src/where.c
+++ src/where.c
@@ -3920,10 +3920,21 @@
 
     /* whereLoopAddBtree() always generates and inserts the automatic index
     ** case first.  Hence compatible candidate WhereLoops never have a larger
     ** rSetup. Call this SETUP-INVARIANT */
     assert( p->rSetup>=pTemplate->rSetup );
+
+    /* Any loop using an appliation-defined index (or PRIMARY KEY or
+    ** UNIQUE constraint) with one or more == constraints is better
+    ** than an automatic index. */
+    if( (p->wsFlags & WHERE_AUTO_INDEX)!=0
+     && (pTemplate->wsFlags & WHERE_INDEXED)!=0
+     && (pTemplate->wsFlags & WHERE_COLUMN_EQ)!=0
+     && (p->prereq & pTemplate->prereq)==pTemplate->prereq
+    ){
+      break;
+    }
 
     /* If existing WhereLoop p is better than pTemplate, pTemplate can be
     ** discarded.  WhereLoop p is better if:
     **   (1)  p has no more dependencies than pTemplate, and
     **   (2)  p has an equal or lower cost than pTemplate
@@ -4045,11 +4056,11 @@
     ** p[] that are also supplated by pTemplate */
     WhereLoop **ppTail = &p->pNextLoop;
     WhereLoop *pToDel;
     while( *ppTail ){
       ppTail = whereLoopFindLesser(ppTail, pTemplate);
-      if( NEVER(ppTail==0) ) break;
+      if( ppTail==0 ) break;
       pToDel = *ppTail;
       if( pToDel==0 ) break;
       *ppTail = pToDel->pNextLoop;
 #if WHERETRACE_ENABLED /* 0x8 */
       if( sqlite3WhereTrace & 0x8 ){

ADDED   test/autoindex3.test
Index: test/autoindex3.test
==================================================================
--- /dev/null
+++ test/autoindex3.test
@@ -0,0 +1,58 @@
+# 2014-06-17
+#
+# 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.
+#
+#*************************************************************************
+#
+# This file implements regression tests for SQLite library.  The
+# focus of this script is testing automatic index creation logic,
+# and specifically that an automatic index will not be created that
+# shadows a declared index.
+#
+
+set testdir [file dirname $argv0]
+source $testdir/tester.tcl
+
+# The t1b and t2d indexes are not very selective.  It used to be that
+# the autoindex mechanism would create automatic indexes on t1(b) or
+# t2(d), make assumptions that they were reasonably selective, and use
+# them instead of t1b or t2d.  But that would be cheating, because the
+# automatic index cannot be any more selective than the real index.
+#
+# This test verifies that the cheat is no longer allowed.
+#
+do_execsql_test autoindex3-100 {
+  CREATE TABLE t1(a,b,x);
+  CREATE TABLE t2(c,d,y);
+  CREATE INDEX t1b ON t1(b);
+  CREATE INDEX t2d ON t2(d);
+  ANALYZE sqlite_master;
+  INSERT INTO sqlite_stat1 VALUES('t1','t1b','10000 500');
+  INSERT INTO sqlite_stat1 VALUES('t2','t2d','10000 500');
+  ANALYZE sqlite_master;
+  EXPLAIN QUERY PLAN SELECT * FROM t1, t2 WHERE d=b;
+} {~/AUTO/}
+
+# Automatic indexes can still be used if existing indexes do not
+# participate in == constraints.
+#
+do_execsql_test autoindex3-110 {
+  EXPLAIN QUERY PLAN SELECT * FROM t1, t2 WHERE d>b AND x=y;
+} {/AUTO/}
+do_execsql_test autoindex3-120 {
+  EXPLAIN QUERY PLAN SELECT * FROM t1, t2 WHERE d<b AND x=y;
+} {/AUTO/}
+do_execsql_test autoindex3-130 {
+  EXPLAIN QUERY PLAN SELECT * FROM t1, t2 WHERE d IS NULL AND x=y;
+} {/AUTO/}
+do_execsql_test autoindex3-140 {
+  EXPLAIN QUERY PLAN SELECT * FROM t1, t2 WHERE d IN (5,b) AND x=y;
+} {/AUTO/}
+
+
+finish_test