diff --git a/Makefile b/Makefile
index 7b07ccd7f6..b7bacca469 100644
--- a/Makefile
+++ b/Makefile
@@ -4,11 +4,15 @@
 
 MAKEFLAGS = -s
 
-all: build unit_test queryservice_test integration_test
+.PHONY: all build test clean unit_test unit_test_cover unit_test_race queryservice_test integration_test bson
+
+all: build test
 
 build:
 	go install ./go/...
 
+test: unit_test queryservice_test integration_test
+
 clean:
 	go clean -i ./go/...
 
diff --git a/go/vt/mysqlctl/mycnf.go b/go/vt/mysqlctl/mycnf.go
index 7c2d1a4c8c..4d42fee8e1 100644
--- a/go/vt/mysqlctl/mycnf.go
+++ b/go/vt/mysqlctl/mycnf.go
@@ -24,24 +24,72 @@ import (
 // populated from an existing my.cnf, or by command line parameters.
 // command line parameters.
 type Mycnf struct {
-	ServerId              uint32
-	MysqlPort             int
-	DataDir               string
-	InnodbDataHomeDir     string
+	// ServerId is the unique id for this server.
+	// Used to create a bunch of named directories.
+	ServerId uint32
+
+	// MysqlPort is the port for the MySQL server running on this machine.
+	// It is mainly used to communicate with topology server.
+	MysqlPort int
+
+	// DataDir is where the table files are
+	// (used by vt software for Clone)
+	DataDir string
+
+	// InnodbDataHomeDir is the data directory for innodb.
+	// (used by vt software for Clone)
+	InnodbDataHomeDir string
+
+	// InnodbLogGroupHomeDir is the logs directory for innodb.
+	// (used by vt software for Clone)
 	InnodbLogGroupHomeDir string
-	SocketFile            string
-	ErrorLogPath          string
-	SlowLogPath           string
-	RelayLogPath          string
-	RelayLogIndexPath     string
-	RelayLogInfoPath      string
-	BinLogPath            string
-	MasterInfoFile        string
-	PidFile               string
-	TmpDir                string
-	SlaveLoadTmpDir       string
-	mycnfMap              map[string]string
-	path                  string // the actual path that represents this mycnf
+
+	// SocketFile is the path to the local mysql.sock file.
+	// (used by vt software to check server is running)
+	SocketFile string
+
+	// ErrorLogPath is the path to store error logs at.
+	// (unused by vt software for now)
+	ErrorLogPath string
+
+	// SlowLogPath is the slow query log path
+	// (unused by vt software for now)
+	SlowLogPath string
+
+	// RelayLogPath is the path of the relay logs
+	// (unused by vt software for now)
+	RelayLogPath string
+
+	// RelayLogIndexPath is the file name for the relay log index
+	// (unused by vt software for now)
+	RelayLogIndexPath string
+
+	// RelayLogInfoPath is the file name for the relay log info file
+	// (unused by vt software for now)
+	RelayLogInfoPath string
+
+	// BinLogPath is the base path for binlogs
+	// (used by vt software for binlog streaming and rowcache invalidation)
+	BinLogPath string
+
+	// MasterInfoFile is the master.info file location.
+	// (unused by vt software for now)
+	MasterInfoFile string
+
+	// PidFile is the mysql.pid file location
+	// (used by vt software to check server is running)
+	PidFile string
+
+	// TmpDir is where to create temporary tables
+	// (unused by vt software for now)
+	TmpDir string
+
+	// SlaveLoadTmpDir is where to create tmp files for replication
+	// (unused by vt software for now)
+	SlaveLoadTmpDir string
+
+	mycnfMap map[string]string
+	path     string // the actual path that represents this mycnf
 }
 
 func (cnf *Mycnf) lookupAndCheck(key string) string {
diff --git a/go/vt/mysqlctl/mysqld.go b/go/vt/mysqlctl/mysqld.go
index 474a04201d..1e0fa46ea4 100644
--- a/go/vt/mysqlctl/mysqld.go
+++ b/go/vt/mysqlctl/mysqld.go
@@ -383,11 +383,6 @@ func deleteTopDir(dir string) (removalErr error) {
 	return
 }
 
-// Port returns the configured mysql port
-func (mysqld *Mysqld) Port() int {
-	return mysqld.config.MysqlPort
-}
-
 // Addr returns the fully qualified host name + port for this instance.
 func (mysqld *Mysqld) Addr() string {
 	hostname := netutil.FullyQualifiedHostnameOrPanic()
diff --git a/go/vt/tabletmanager/agent.go b/go/vt/tabletmanager/agent.go
index 6fb0fc94ee..edb1ac2bec 100644
--- a/go/vt/tabletmanager/agent.go
+++ b/go/vt/tabletmanager/agent.go
@@ -141,7 +141,18 @@ func NewActionAgent(
 	agent.BinlogPlayerMap = NewBinlogPlayerMap(topoServer, &dbcfgs.App.ConnectionParams, mysqld)
 	RegisterBinlogPlayerMap(agent.BinlogPlayerMap)
 
-	if err := agent.Start(mysqld.Port(), port, securePort); err != nil {
+	// try to figure out the mysql port
+	mysqlPort := mycnf.MysqlPort
+	if mysqlPort == 0 {
+		// we don't know the port, try to get it from mysqld
+		var err error
+		mysqlPort, err = mysqld.GetMysqlPort()
+		if err != nil {
+			log.Warningf("Cannot get current mysql port, will use 0 for now: %v", err)
+		}
+	}
+
+	if err := agent.Start(mysqlPort, port, securePort); err != nil {
 		return nil, err
 	}
 
@@ -376,7 +387,11 @@ func (agent *ActionAgent) Start(mysqlPort, vtPort, vtsPort int) error {
 		if tablet.Portmap == nil {
 			tablet.Portmap = make(map[string]int)
 		}
-		tablet.Portmap["mysql"] = mysqlPort
+		if mysqlPort != 0 {
+			// only overwrite mysql port if we know it, otherwise
+			// leave it as is.
+			tablet.Portmap["mysql"] = mysqlPort
+		}
 		tablet.Portmap["vt"] = vtPort
 		if vtsPort != 0 {
 			tablet.Portmap["vts"] = vtsPort