Let disabled targets be ignored during normal operation:

 - In target_examine(), ignore disabled TAPs

 - Reset handling must not poke at them either:
     * fail $target_name arp_* operations on disabled TAPs
     * in startup.tcl, don't even issue the arp_* wait ops

No other target cleanup included here.
---
 src/helper/startup.tcl |   28 +++++++++++++++++++++++-----
 src/target/target.c    |   27 ++++++++++++++++++++++++---
 2 files changed, 47 insertions(+), 8 deletions(-)

Let disabled targets be ignored during normal operation:

 - In target_examine(), ignore disabled TAPs

 - Reset handling must not poke at them either:
     * fail $target_name arp_* operations on disabled TAPs
     * in startup.tcl, don't even issue the arp_* wait ops 

No other target cleanup included here.
---
 src/helper/startup.tcl |   28 +++++++++++++++++++++++-----
 src/target/target.c    |   27 ++++++++++++++++++++++++---
 2 files changed, 47 insertions(+), 8 deletions(-)

--- a/src/helper/startup.tcl
+++ b/src/helper/startup.tcl
@@ -164,6 +164,11 @@ proc ocd_process_reset { MODE } {
 		return -error "Invalid mode: $MODE, must be one of: halt, init, or run";
 	}
 
+	# Target event handlers *might* change which TAPs are enabled
+	# or disabled, so we fire all of them.  But don't issue any
+	# of the "arp_*" commands, which may issue JTAG transactions,
+	# unless we know the underlying TAP is active.
+
 	foreach t [ target names ] {
 		# New event script.
 		$t invoke-event reset-start
@@ -172,16 +177,20 @@ proc ocd_process_reset { MODE } {
 	# Init the tap controller.
 	jtag arp_init-reset
 
-	# Examine all targets.
+	# Examine all targets on enabled taps.
 	foreach t [ target names ] {
-		$t arp_examine
+		if {[jtag tapisenabled [$t cget -chain-position]]} {
+			$t arp_examine
+		}
 	}
 
 	# Let the C code know we are asserting reset.
 	foreach t [ target names ] {
 		$t invoke-event reset-assert-pre
 		# C code needs to know if we expect to 'halt'
-		$t arp_reset assert $halt
+		if {[jtag tapisenabled [$t cget -chain-position]]} {
+			$t arp_reset assert $halt
+		}
 		$t invoke-event reset-assert-post
 	}
 
@@ -189,14 +198,19 @@ proc ocd_process_reset { MODE } {
 	foreach t [ target names ] {
 		$t invoke-event reset-deassert-pre
 		# Again, de-assert code needs to know..
-		$t arp_reset deassert $halt
+		if {[jtag tapisenabled [$t cget -chain-position]]} {
+			$t arp_reset deassert $halt
+		}
 		$t invoke-event reset-deassert-post
 	}
 
 	# Pass 1 - Now try to halt.
 	if { $halt } {
 		foreach t [target names] {
-	
+			if {[jtag tapisenabled [$t cget -chain-position]] == 0} {
+				continue
+			}
+
 			# Wait upto 1 second for target to halt.  Why 1sec? Cause
 			# the JTAG tap reset signal might be hooked to a slow
 			# resistor/capacitor circuit - and it might take a while
@@ -217,6 +231,10 @@ proc ocd_process_reset { MODE } {
 	#Pass 2 - if needed "init"
 	if { 0 == [string compare init $MODE] } {
 		foreach t [target names] {
+			if {[jtag tapisenabled [$t cget -chain-position]] == 0} {
+				continue
+			}
+
 			set err [catch "$t arp_waitstate halted 5000"]
 			# Did it halt?
 			if { $err == 0 } {
--- a/src/target/target.c
+++ b/src/target/target.c
@@ -479,12 +479,14 @@ int target_examine_one(struct target_s *
 int target_examine(void)
 {
 	int retval = ERROR_OK;
-	target_t *target = all_targets;
-	while (target)
+	target_t *target;
+
+	for (target = all_targets; target; target = target->next)
 	{
+		if (!target->tap->enabled)
+			continue;
 		if ((retval = target_examine_one(target)) != ERROR_OK)
 			return retval;
-		target = target->next;
 	}
 	return retval;
 }
@@ -3734,6 +3736,9 @@ static int tcl_target_func( Jim_Interp *
 			Jim_WrongNumArgs( goi.interp, 2, argv, "[no parameters]");
 			return JIM_ERR;
 		}
+		if (!target->tap->enabled) {
+			goto err_tap_disabled;
+		}
 		e = target->type->examine( target );
 		if( e != ERROR_OK ){
 			Jim_SetResult_sprintf( interp, "examine-fails: %d", e );
@@ -3745,6 +3750,9 @@ static int tcl_target_func( Jim_Interp *
 			Jim_WrongNumArgs( goi.interp, 2, argv, "[no parameters]");
 			return JIM_ERR;
 		}
+		if (!target->tap->enabled) {
+			goto err_tap_disabled;
+		}
 		if( !(target_was_examined(target)) ){
 			e = ERROR_TARGET_NOT_EXAMINED;
 		} else {
@@ -3772,6 +3780,9 @@ static int tcl_target_func( Jim_Interp *
 		if( e != JIM_OK ){
 			return e;
 		}
+		if (!target->tap->enabled) {
+			goto err_tap_disabled;
+		}
 		/* determine if we should halt or not. */
 		target->reset_halt = !!a;
 		/* When this happens - all workareas are invalid. */
@@ -3789,6 +3800,9 @@ static int tcl_target_func( Jim_Interp *
 			Jim_WrongNumArgs( goi.interp, 0, argv, "halt [no parameters]");
 			return JIM_ERR;
 		}
+		if (!target->tap->enabled) {
+			goto err_tap_disabled;
+		}
 		target->type->halt( target );
 		return JIM_OK;
 	case TS_CMD_WAITSTATE:
@@ -3806,6 +3820,9 @@ static int tcl_target_func( Jim_Interp *
 		if( e != JIM_OK ){
 			return e;
 		}
+		if (!target->tap->enabled) {
+			goto err_tap_disabled;
+		}
 		e = target_wait_state( target, n->value, a );
 		if( e != ERROR_OK ){
 			Jim_SetResult_sprintf( goi.interp,
@@ -3861,6 +3878,10 @@ static int tcl_target_func( Jim_Interp *
 		return JIM_OK;
 	}
 	return JIM_ERR;
+
+err_tap_disabled:
+	Jim_SetResult_sprintf(interp, "[TAP is disabled]");
+	return JIM_ERR;
 }
 
 static int target_create( Jim_GetOptInfo *goi )
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