diff --git a/src/counters.c b/src/counters.c
index 37f836a952..f4fca5c0d4 100644
--- a/src/counters.c
+++ b/src/counters.c
@@ -15,12 +15,11 @@
 /** \todo config api */
 #define LOGPATH "/var/log/eidps/stats.log"
 
-static PerfThreadContext *perf_tc = NULL;
 static PerfOPIfaceContext *perf_op_ctx = NULL;
 
 /**
- * Initializes the perf counter api.  Things are hard coded currently.
- * More work to be done when we implement multiple interfaces
+ * \brief Initializes the perf counter api.  Things are hard coded currently.
+ *        More work to be done when we implement multiple interfaces
  */
 void PerfInitCounterApi()
 {
@@ -30,7 +29,7 @@ void PerfInitCounterApi()
 }
 
 /**
- * Initializes the output interface context
+ * \brief Initializes the output interface context
  */
 void PerfInitOPCtx()
 {
@@ -65,92 +64,49 @@ void PerfInitOPCtx()
 }
 
 /**
- * Spawns the wakeup, and the management thread
+ * \brief Spawns the wakeup, and the management thread
  */
 void PerfSpawnThreads()
 {
-    pthread_attr_t attr;
-
-    pthread_attr_init(&attr);
-    pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
-
-    printf("PerfSpawnThreads: spawning counter threads\n");
-
-    if ( (perf_tc = malloc(sizeof(PerfThreadContext))) == NULL) {
-        printf("Error allocating memory\n");
-        exit(0);
+    ThreadVars *tv_wakeup = NULL;
+    ThreadVars *tv_mgmt = NULL;
+
+    /* Spawn the stats wakeup thread */
+    tv_wakeup = TmThreadCreate("PerfWakeupThread", NULL, NULL, NULL, NULL,
+                               "custom", PerfWakeupThread, 1);
+    if (tv_wakeup == NULL) {
+        printf("ERROR: TmThreadsCreate failed\n");
+        exit(1);
     }
-    memset(perf_tc, 0, sizeof(PerfThreadContext));
-
-    perf_tc->flags = PT_RUN;
-
-    if (pthread_mutex_init(&perf_tc->wakeup_m, NULL) != 0) {
-        printf("Error initializing the perf_tc->wakeup_m mutex\n");
-        exit(0);
+    if (TmThreadSpawn(tv_wakeup, TVT_MGMT, THV_USE | THV_PAUSE) != 0) {
+        printf("ERROR: TmThreadSpawn failed\n");
+        exit(1);
     }
 
-    if (pthread_mutex_init(&perf_tc->mgmt_m, NULL) != 0) {
-        printf("Error initializing the perf_tc->mgmt_m mutex\n");
-        exit(0);
+    /* Spawn the stats mgmt thread */
+    tv_mgmt = TmThreadCreate("PerfMgmtThread", NULL, NULL, NULL, NULL,
+                             "custom", PerfMgmtThread, 1);
+    if (tv_mgmt == NULL) {
+        printf("ERROR: TmThreadsCreate failed\n");
+        exit(1);
     }
-
-    if (pthread_cond_init(&perf_tc->tc_cond, NULL) != 0) {
-        printf("Error initializing the perf_tc->tc_cond condition variable\n");
-        exit(0);
-    }
-
-    if (pthread_create(&perf_tc->wakeup_t, &attr, PerfWakeupThread, NULL) != 0) {
-        printf("Error creating PerfWakeupFunc thread\n");
-        exit(0);
-    }
-
-    if (pthread_create(&perf_tc->mgmt_t, &attr, PerfMgmtThread, NULL) != 0) {
-        printf("Error creating PerfWakeupFunc thread\n");
-        exit(0);
+    if (TmThreadSpawn(tv_mgmt, TVT_MGMT, THV_USE | THV_PAUSE) != 0) {
+        printf("ERROR: TmThreadSpawn failed\n");
+        exit(1);
     }
 
     return;
 }
 
 /**
- * Kills the wakeup and the management threads
- */
-void PerfDestroyThreads()
-{
-    perf_tc->flags |= PT_KILL;
-
-    /* prematurely wakeup, the mgmt and wakeup threads */
-    pthread_cond_broadcast(&perf_tc->tc_cond);
-
-    pthread_join(perf_tc->wakeup_t, NULL);
-    pthread_join(perf_tc->mgmt_t, NULL);
-
-    if (pthread_mutex_destroy(&perf_tc->wakeup_m) != 0) {
-        printf("Error destroying the mutex perf_tc->wakeup_m\n");
-    }
-
-    if (pthread_mutex_destroy(&perf_tc->mgmt_m) != 0) {
-        printf("Error destroying the mutex perf_tc->mgmt_m\n");
-    }
-
-    if (pthread_cond_destroy(&perf_tc->tc_cond) != 0) {
-        printf("Error destroying the condition variable perf_tc->tc_cond\n");
-    }
-
-    if (perf_tc != NULL) free(perf_tc);
-
-    return;
-}
-
-
-/**
- * The management thread. This thread is responsible for writing the performance
- * stats information.
+ * \brief The management thread. This thread is responsible for writing the
+ *        performance stats information.
  *
- * @param arg is NULL always
+ * \param arg is NULL always
  */
 void * PerfMgmtThread(void *arg)
 {
+    ThreadVars *tv_local = (ThreadVars *)arg;
     u_int8_t run = 1;
     struct timespec cond_time;
 
@@ -162,33 +118,37 @@ void * PerfMgmtThread(void *arg)
     }
 
     while (run) {
+        TmThreadTestThreadUnPaused(tv_local);
+
         cond_time.tv_sec = time(NULL) + MGMTT_TTS;
         cond_time.tv_nsec = 0;
 
-        pthread_mutex_lock(&perf_tc->mgmt_m);
-        pthread_cond_timedwait(&perf_tc->tc_cond, &perf_tc->mgmt_m,
-                               &cond_time);
-        pthread_mutex_unlock(&perf_tc->mgmt_m);
+        pthread_mutex_lock(tv_local->m);
+        pthread_cond_timedwait(tv_local->cond, tv_local->m, &cond_time);
+        pthread_mutex_unlock(tv_local->m);
 
         // sleep(MGMTT_TTS);
 
         PerfOutputCounters();
 
-        if (perf_tc->flags & PT_KILL)
+        if (tv_local->flags & THV_KILL) {
+            tv_local->flags |= THV_CLOSED;
             run = 0;
+        }
     }
 
     return NULL;
 }
 
 /**
- * Wake up thread.  This thread wakes up every TTS(time to sleep) seconds and
- * sets the flag for every ThreadVars' PerfContext
+ * \brief Wake up thread.  This thread wakes up every TTS(time to sleep) seconds
+ *        and sets the flag for every ThreadVars' PerfContext
  *
- * @param arg is NULL always
+ * \param arg is NULL always
  */
 void * PerfWakeupThread(void *arg)
 {
+    ThreadVars *tv_local = (ThreadVars *)arg;
     u_int8_t run = 1;
     ThreadVars *tv = NULL;
     PacketQueue *q = NULL;
@@ -197,18 +157,18 @@ void * PerfWakeupThread(void *arg)
     printf("PerfWakeupThread: spawned\n");
 
     while (run) {
+        TmThreadTestThreadUnPaused(tv_local);
+
         cond_time.tv_sec = time(NULL) + WUT_TTS;
         cond_time.tv_nsec = 0;
 
-        pthread_mutex_lock(&perf_tc->wakeup_m);
-        pthread_cond_timedwait(&perf_tc->tc_cond, &perf_tc->wakeup_m,
-                               &cond_time);
-        pthread_mutex_unlock(&perf_tc->wakeup_m);
+        pthread_mutex_lock(tv_local->m);
+        pthread_cond_timedwait(tv_local->cond, tv_local->m, &cond_time);
+        pthread_mutex_unlock(tv_local->m);
 
         // sleep(WUT_TTS);
 
-        tv = tv_root;
-
+        tv = tv_root[TVT_PPT];
         while (tv != NULL) {
             if (tv->inq == NULL || tv->pctx.head == NULL) {
                 tv = tv->next;
@@ -226,23 +186,26 @@ void * PerfWakeupThread(void *arg)
             tv = tv->next;
         }
 
-        if (perf_tc->flags & PT_KILL)
+        if (tv_local->flags & THV_KILL) {
+            tv_local->flags |= THV_CLOSED;
             run = 0;
+        }
     }
 
     return NULL;
 }
 
 /**
- *  Registers a counter
+ * \brief Registers a counter
  *
- * @param cname holds the counter name
- * @param tm_name holds the tm_name
- * @param tid holds the tid running this module
- * @param type holds the datatype of this counter variable
- * @param head holds the PerfCounter
+ * \param cname   Counter name to be registered
+ * \param tm_name Thread module name
+ * \param tid     Thread id running this module instance
+ * \param type    Datatype of this counter variable
+ * \param desc    Description of this counter
+ * \param pctx    PerfContext for this tm-tv instance
  *
- * @returns the counter id
+ * \retval the counter id
  */
 u_int32_t PerfRegisterCounter(char *cname, char *tm_name, int type,
                               char *desc, PerfContext *pctx)
@@ -335,11 +298,11 @@ u_int32_t PerfRegisterCounter(char *cname, char *tm_name, int type,
 }
 
 /**
- * Adds a TM to the clubbed TM table.  Multiple instances of the same TM are
- * stacked together in a PCTMI container
+ * \brief Adds a TM to the clubbed TM table.  Multiple instances of the same TM
+ *        are stacked together in a PCTMI container
  *
- * @param tm_name is the name of the tm to be added
- * @param pctx holds the PerfContext associated with the TM tm_name
+ * \param tm_name Name of the tm to be added to the table
+ * \param pctx    PerfContext associated with the TM tm_name
  */
 void PerfAddToClubbedTMTable(char *tm_name, PerfContext *pctx)
 {
@@ -414,13 +377,13 @@ void PerfAddToClubbedTMTable(char *tm_name, PerfContext *pctx)
 
 
 /**
- * Returns a counter array for counters in this id range(s_id - e_id)
+ * \brief Returns a counter array for counters in this id range(s_id - e_id)
  *
- * @param s_id is the start id of the counter
- * @param e_id is the end id of the counter
- * @param pctx is a pointer to the tv's PerfContext
+ * \param s_id Counter id of the first counter to be added to the array
+ * \param e_id Counter id of the last counter to be added to the array
+ * \param pctx Pointer to the tv's PerfContext
  *
- * @returns a counter-array in this(s_id-e_id) range for this tm instance
+ * \retval a counter-array in this(s_id-e_id) range for this TM instance
  */
 PerfCounterArray * PerfGetCounterArrayRange(u_int32_t s_id, u_int32_t e_id,
                                             PerfContext *pctx)
@@ -471,11 +434,11 @@ PerfCounterArray * PerfGetCounterArrayRange(u_int32_t s_id, u_int32_t e_id,
 }
 
 /**
- * Returns a counter array for all counters registered for this tm instance
+ * \brief Returns a counter array for all counters registered for this tm instance
  *
- * @param pctx is a pointer to the tv's PerfContext
+ * \param pctx Pointer to the tv's PerfContext
  *
- * @returns a counter-array for all the counters of this tm instance
+ * \retval a counter-array for all counters of this tm instance
  */
 PerfCounterArray * PerfGetAllCountersArray(PerfContext *pctx)
 {
@@ -484,13 +447,15 @@ PerfCounterArray * PerfGetAllCountersArray(PerfContext *pctx)
 
 
 /**
- * Updates an individual counter
+ * \brief Updates an individual counter
+ *
+ * \param cname    Name of the counter to be synced
+ * \param tm_name  Thread module name
+ * \param id holds Counter id of the counter to be synced
+ * \param value    Pointer to the local counter from the client thread
+ * \param pctx     PerfContext for this tm-tv instance
  *
- * @param cname holds the counter name
- * @param tm_name holds the tm name
- * @param id holds the counter id for this tm
- * @param value holds a pointer to the local counter from the client thread
- * @param pctx holds the PerfContext associated with this instance of the tm
+ * \retval 1 on success, 0 on failure
  */
 int PerfUpdateCounter(char *cname, char *tm_name, u_int32_t id, void *value,
                       PerfContext *pctx)
@@ -535,11 +500,11 @@ int PerfUpdateCounter(char *cname, char *tm_name, u_int32_t id, void *value,
 }
 
 /**
- * Syncs the counter array with the global counter variables
+ * \brief Syncs the counter array with the global counter variables
  *
- * @param pca holds a pointer to the PerfCounterArray
- * @param pctx holds a pointer the the tv's PerfContext
- * @param reset_lc indicates whether the local counter has to be reset or not
+ * \param pca      Pointer to the PerfCounterArray
+ * \param pctx     Pointer the the tv's PerfContext
+ * \param reset_lc Indicates whether the local counter has to be reset or not
  */
 int PerfUpdateCounterArray(PerfCounterArray *pca, PerfContext *pctx, int reset_lc)
 {
@@ -582,7 +547,7 @@ int PerfUpdateCounterArray(PerfCounterArray *pca, PerfContext *pctx, int reset_l
 }
 
 /**
- * The output interface dispatcher for the counter api
+ * \brief The output interface dispatcher for the counter api
  */
 void PerfOutputCounters()
 {
@@ -605,11 +570,11 @@ void PerfOutputCounters()
 }
 
 /**
- * The file output interface for the counter api
+ * \brief The file output interface for the counter api
  */
 int PerfOutputCounterFileIface()
 {
-    ThreadVars *tv = tv_root;
+    ThreadVars *tv = NULL;
     PerfClubTMInst *pctmi = NULL;
     PerfCounter *pc = NULL;
     PerfCounter **pc_heads;
@@ -645,25 +610,28 @@ int PerfOutputCounterFileIface()
             "------------------\n");
 
     if (perf_op_ctx->club_tm == 0) {
-        while (tv != NULL) {
-            pthread_mutex_lock(&tv->pctx.m);
-            pc = tv->pctx.head;
-
-            while (pc != NULL) {
-                ui64_cvalue = (u_int64_t *)pc->value->cvalue;
-                fprintf(perf_op_ctx->fp, "%-25s | %-25s | %-llu\n",
-                        pc->name->cname, pc->name->tm_name, *ui64_cvalue);
-                //printf("%-10d %-10d %-10s %-llu\n", pc->name->tid, pc->id,
-                //       pc->name->cname, *ui64_cvalue);
-                pc = pc->next;
+        for (i = 0; i < TVT_MAX; i++) {
+            tv = tv_root[i];
+
+            while (tv != NULL) {
+                pthread_mutex_lock(&tv->pctx.m);
+                pc = tv->pctx.head;
+
+                while (pc != NULL) {
+                    ui64_cvalue = (u_int64_t *)pc->value->cvalue;
+                    fprintf(perf_op_ctx->fp, "%-25s | %-25s | %-llu\n",
+                            pc->name->cname, pc->name->tm_name, *ui64_cvalue);
+                    //printf("%-10d %-10d %-10s %-llu\n", pc->name->tid, pc->id,
+                    //       pc->name->cname, *ui64_cvalue);
+                    pc = pc->next;
+                }
+
+                pthread_mutex_unlock(&tv->pctx.m);
+                tv = tv->next;
             }
-
-            pthread_mutex_unlock(&tv->pctx.m);
-            tv = tv->next;
+            fflush(perf_op_ctx->fp);
         }
 
-        fflush(perf_op_ctx->fp);
-
         return 1;
     }
 
@@ -717,12 +685,10 @@ int PerfOutputCounterFileIface()
 }
 
 /**
- * Kills the perf threads and releases other resources.
+ * \brief Releases perf api resources.
  */
 void PerfReleaseResources()
 {
-    PerfDestroyThreads();
-
     PerfReleaseOPCtx();
 
     return;
diff --git a/src/counters.h b/src/counters.h
index c979c1a150..acaa8c9d1f 100644
--- a/src/counters.h
+++ b/src/counters.h
@@ -1,4 +1,4 @@
-/** Copyright (c) Open Information Security Foundation.
+/** Copyright (c) 2009 Open Information Security Foundation.
  *  \author Anoop Saldanha <poonaatsoc@gmail.com>
  */
 
@@ -6,14 +6,11 @@
 #define __COUNTERS_H__
 
 
-/** Time interval for syncing the local counters with the global ones */
+/* Time interval for syncing the local counters with the global ones */
 #define WUT_TTS 3
-/** Time interval at which the mgmt thread o/p the stats */
+/* Time interval at which the mgmt thread o/p the stats */
 #define MGMTT_TTS 8
 
-#define PT_RUN 0x01
-#define PT_KILL 0x02
-
 /* These 2 macros can only be used when all the registered counters for the tm,
  * are in the counter array */
 #define PerfCounterIncr(id, pca) do { \
@@ -54,21 +51,6 @@ enum {
     IFACE_SYSLOG,
 };
 
-/* Holds the thread context for the counter api */
-typedef struct _PerfThreadContext {
-    pthread_t wakeup_t;
-    pthread_t mgmt_t;
-
-    /* state of the 2 threads, determined by PT_RUN AND PT_KILL */
-    u_int32_t flags;
-
-    /* need these mutexes just for calling pthread_cond_timewait() on tc_cond */
-    pthread_mutex_t wakeup_m;
-    pthread_mutex_t mgmt_m;
-
-    pthread_cond_t tc_cond;
-} PerfThreadContext;
-
 typedef struct _PerfCounterName {
     char *cname;
     char *tm_name;
@@ -156,8 +138,6 @@ void PerfInitOPCtx(void);
 
 void PerfSpawnThreads(void);
 
-void PerfDestroyThreads(void);
-
 void * PerfMgmtThread(void *);
 
 void * PerfWakeupThread(void *);
diff --git a/src/eidps.c b/src/eidps.c
index 41e082d2af..a0d40e9d18 100644
--- a/src/eidps.c
+++ b/src/eidps.c
@@ -58,12 +58,12 @@
 #include "flow-bit.h"
 #include "pkt-var.h"
 
+#include "l7-app-detect.h"
+
 #include "util-cidr.h"
 #include "util-unittest.h"
 #include "util-time.h"
 
-pthread_attr_t attr;
-
 /*
  * we put this here, because we only use it here in main.
  */
@@ -202,7 +202,7 @@ int RunModeIdsPcap(char *iface) {
     TimeModeSetLive();
 
     /* create the threads */
-    ThreadVars *tv_receivepcap = TmThreadCreate("ReceivePcap","packetpool","packetpool","pickup-queue","simple","1slot_noinout");
+    ThreadVars *tv_receivepcap = TmThreadCreate("ReceivePcap","packetpool","packetpool","pickup-queue","simple","1slot_noinout", NULL, 0);
     if (tv_receivepcap == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -214,12 +214,12 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm1SlotSetFunc(tv_receivepcap,tm_module,(void *)iface);
 
-    if (TmThreadSpawn(tv_receivepcap) != 0) {
+    if (TmThreadSpawn(tv_receivepcap, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_decode1 = TmThreadCreate("Decode1","pickup-queue","simple","decode-queue1","simple","1slot");
+    ThreadVars *tv_decode1 = TmThreadCreate("Decode1","pickup-queue","simple","decode-queue1","simple","1slot", NULL, 0);
     if (tv_decode1 == NULL) {
         printf("ERROR: TmThreadsCreate failed for Decode1\n");
         exit(1);
@@ -231,12 +231,12 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm1SlotSetFunc(tv_decode1,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_decode1) != 0) {
+    if (TmThreadSpawn(tv_decode1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_stream1 = TmThreadCreate("Stream1","decode-queue1","simple","stream-queue1","simple","1slot");
+    ThreadVars *tv_stream1 = TmThreadCreate("Stream1","decode-queue1","simple","stream-queue1","simple","1slot", NULL, 0);
     if (tv_stream1 == NULL) {
         printf("ERROR: TmThreadsCreate failed for Stream1\n");
         exit(1);
@@ -248,12 +248,12 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm1SlotSetFunc(tv_stream1,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_stream1) != 0) {
+    if (TmThreadSpawn(tv_stream1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_detect1 = TmThreadCreate("Detect1","stream-queue1","simple","verdict-queue","simple","1slot");
+    ThreadVars *tv_detect1 = TmThreadCreate("Detect1","stream-queue1","simple","verdict-queue","simple","1slot", NULL, 0);
     if (tv_detect1 == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -265,12 +265,12 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm1SlotSetFunc(tv_detect1,tm_module,(void *)g_de_ctx);
 
-    if (TmThreadSpawn(tv_detect1) != 0) {
+    if (TmThreadSpawn(tv_detect1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_detect2 = TmThreadCreate("Detect2","stream-queue1","simple","verdict-queue","simple","1slot");
+    ThreadVars *tv_detect2 = TmThreadCreate("Detect2","stream-queue1","simple","verdict-queue","simple","1slot", NULL, 0);
     if (tv_detect2 == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -282,12 +282,12 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm1SlotSetFunc(tv_detect2,tm_module,(void *)g_de_ctx);
 
-    if (TmThreadSpawn(tv_detect2) != 0) {
+    if (TmThreadSpawn(tv_detect2, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_rreject = TmThreadCreate("RespondReject","verdict-queue","simple","alert-queue1","simple","1slot");
+    ThreadVars *tv_rreject = TmThreadCreate("RespondReject","verdict-queue","simple","alert-queue1","simple","1slot", NULL, 0);
     if (tv_rreject == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -299,12 +299,12 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm1SlotSetFunc(tv_rreject,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_rreject) != 0) {
+    if (TmThreadSpawn(tv_rreject, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_alert = TmThreadCreate("AlertFastlog&Httplog","alert-queue1","simple","alert-queue2","simple","2slot");
+    ThreadVars *tv_alert = TmThreadCreate("AlertFastlog&Httplog","alert-queue1","simple","alert-queue2","simple","2slot", NULL, 0);
     if (tv_alert == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -323,12 +323,12 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm2SlotSetFunc2(tv_alert,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_alert) != 0) {
+    if (TmThreadSpawn(tv_alert, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_unified = TmThreadCreate("AlertUnifiedLog","alert-queue2","simple","alert-queue3","simple","2slot");
+    ThreadVars *tv_unified = TmThreadCreate("AlertUnifiedLog","alert-queue2","simple","alert-queue3","simple","2slot", NULL, 0);
     if (tv_unified == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -348,13 +348,12 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm2SlotSetFunc2(tv_unified,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_unified) != 0) {
+    if (TmThreadSpawn(tv_unified, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-
-    ThreadVars *tv_debugalert = TmThreadCreate("AlertDebuglog","alert-queue3","simple","packetpool","packetpool","1slot");
+    ThreadVars *tv_debugalert = TmThreadCreate("AlertDebuglog","alert-queue3","simple","packetpool","packetpool","1slot", NULL, 0);
     if (tv_debugalert == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -366,7 +365,7 @@ int RunModeIdsPcap(char *iface) {
     }
     Tm1SlotSetFunc(tv_debugalert,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_debugalert) != 0) {
+    if (TmThreadSpawn(tv_debugalert, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
@@ -378,7 +377,7 @@ int RunModeIpsNFQ(void) {
     TimeModeSetLive();
 
     /* create the threads */
-    ThreadVars *tv_receivenfq = TmThreadCreate("ReceiveNFQ","packetpool","packetpool","pickup-queue","simple","1slot_noinout");
+    ThreadVars *tv_receivenfq = TmThreadCreate("ReceiveNFQ","packetpool","packetpool","pickup-queue","simple","1slot_noinout", NULL, 0);
     if (tv_receivenfq == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -390,12 +389,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm1SlotSetFunc(tv_receivenfq,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_receivenfq) != 0) {
+    if (TmThreadSpawn(tv_receivenfq, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_decode1 = TmThreadCreate("Decode1","pickup-queue","simple","decode-queue1","simple","1slot");
+    ThreadVars *tv_decode1 = TmThreadCreate("Decode1","pickup-queue","simple","decode-queue1","simple","1slot", NULL, 0);
     if (tv_decode1 == NULL) {
         printf("ERROR: TmThreadsCreate failed for Decode1\n");
         exit(1);
@@ -407,12 +406,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm1SlotSetFunc(tv_decode1,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_decode1) != 0) {
+    if (TmThreadSpawn(tv_decode1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_stream1 = TmThreadCreate("Stream1","decode-queue1","simple","stream-queue1","simple","1slot");
+    ThreadVars *tv_stream1 = TmThreadCreate("Stream1","decode-queue1","simple","stream-queue1","simple","1slot", NULL, 0);
     if (tv_stream1 == NULL) {
         printf("ERROR: TmThreadsCreate failed for Stream1\n");
         exit(1);
@@ -424,12 +423,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm1SlotSetFunc(tv_stream1,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_stream1) != 0) {
+    if (TmThreadSpawn(tv_stream1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_detect1 = TmThreadCreate("Detect1","stream-queue1","simple","verdict-queue","simple","1slot");
+    ThreadVars *tv_detect1 = TmThreadCreate("Detect1","stream-queue1","simple","verdict-queue","simple","1slot", NULL, 0);
     if (tv_detect1 == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -441,12 +440,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm1SlotSetFunc(tv_detect1,tm_module,(void *)g_de_ctx);
 
-    if (TmThreadSpawn(tv_detect1) != 0) {
+    if (TmThreadSpawn(tv_detect1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_detect2 = TmThreadCreate("Detect2","stream-queue1","simple","verdict-queue","simple","1slot");
+    ThreadVars *tv_detect2 = TmThreadCreate("Detect2","stream-queue1","simple","verdict-queue","simple","1slot", NULL, 0);
     if (tv_detect2 == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -458,12 +457,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm1SlotSetFunc(tv_detect2,tm_module,(void *)g_de_ctx);
 
-    if (TmThreadSpawn(tv_detect2) != 0) {
+    if (TmThreadSpawn(tv_detect2, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_verdict = TmThreadCreate("Verdict","verdict-queue","simple","respond-queue","simple","1slot");
+    ThreadVars *tv_verdict = TmThreadCreate("Verdict","verdict-queue","simple","respond-queue","simple","1slot", NULL, 0);
     if (tv_verdict == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -475,12 +474,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm1SlotSetFunc(tv_verdict,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_verdict) != 0) {
+    if (TmThreadSpawn(tv_verdict, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_rreject = TmThreadCreate("RespondReject","respond-queue","simple","alert-queue1","simple","1slot");
+    ThreadVars *tv_rreject = TmThreadCreate("RespondReject","respond-queue","simple","alert-queue1","simple","1slot", NULL, 0);
     if (tv_rreject == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -492,12 +491,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm1SlotSetFunc(tv_rreject,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_rreject) != 0) {
+    if (TmThreadSpawn(tv_rreject, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_alert = TmThreadCreate("AlertFastlog&Httplog","alert-queue1","simple","alert-queue2","simple","2slot");
+    ThreadVars *tv_alert = TmThreadCreate("AlertFastlog&Httplog","alert-queue1","simple","alert-queue2","simple","2slot", NULL, 0);
     if (tv_alert == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -516,12 +515,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm2SlotSetFunc2(tv_alert,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_alert) != 0) {
+    if (TmThreadSpawn(tv_alert, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_unified = TmThreadCreate("AlertUnifiedLog","alert-queue2","simple","alert-queue3","simple","2slot");
+    ThreadVars *tv_unified = TmThreadCreate("AlertUnifiedLog","alert-queue2","simple","alert-queue3","simple","2slot", NULL, 0);
     if (tv_unified == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -541,13 +540,12 @@ int RunModeIpsNFQ(void) {
     }
     Tm2SlotSetFunc2(tv_unified,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_unified) != 0) {
+    if (TmThreadSpawn(tv_unified, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-
-    ThreadVars *tv_debugalert = TmThreadCreate("AlertDebuglog","alert-queue3","simple","packetpool","packetpool","1slot");
+    ThreadVars *tv_debugalert = TmThreadCreate("AlertDebuglog","alert-queue3","simple","packetpool","packetpool","1slot", NULL, 0);
     if (tv_debugalert == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -559,7 +557,7 @@ int RunModeIpsNFQ(void) {
     }
     Tm1SlotSetFunc(tv_debugalert,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_debugalert) != 0) {
+    if (TmThreadSpawn(tv_debugalert, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
@@ -572,7 +570,7 @@ int RunModeFilePcap(char *file) {
     TimeModeSetOffline();
 
     /* create the threads */
-    ThreadVars *tv_receivepcap = TmThreadCreate("ReceivePcapFile","packetpool","packetpool","pickup-queue","simple","1slot");
+    ThreadVars *tv_receivepcap = TmThreadCreate("ReceivePcapFile","packetpool","packetpool","pickup-queue","simple","1slot", NULL, 0);
     if (tv_receivepcap == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -584,12 +582,12 @@ int RunModeFilePcap(char *file) {
     }
     Tm1SlotSetFunc(tv_receivepcap,tm_module,file);
 
-    if (TmThreadSpawn(tv_receivepcap) != 0) {
+    if (TmThreadSpawn(tv_receivepcap, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_decode1 = TmThreadCreate("Decode1","pickup-queue","simple","decode-queue1","simple","1slot");
+    ThreadVars *tv_decode1 = TmThreadCreate("Decode1","pickup-queue","simple","decode-queue1","simple","1slot", NULL, 0);
     if (tv_decode1 == NULL) {
         printf("ERROR: TmThreadsCreate failed for Decode1\n");
         exit(1);
@@ -601,12 +599,12 @@ int RunModeFilePcap(char *file) {
     }
     Tm1SlotSetFunc(tv_decode1,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_decode1) != 0) {
+    if (TmThreadSpawn(tv_decode1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 //#if 0
-    ThreadVars *tv_stream1 = TmThreadCreate("Stream1","decode-queue1","simple","stream-queue1","simple","1slot");
+    ThreadVars *tv_stream1 = TmThreadCreate("Stream1","decode-queue1","simple","stream-queue1","simple","1slot", NULL, 0);
     if (tv_stream1 == NULL) {
         printf("ERROR: TmThreadsCreate failed for Stream1\n");
         exit(1);
@@ -618,12 +616,12 @@ int RunModeFilePcap(char *file) {
     }
     Tm1SlotSetFunc(tv_stream1,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_stream1) != 0) {
+    if (TmThreadSpawn(tv_stream1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_detect1 = TmThreadCreate("Detect1","stream-queue1","simple","alert-queue1","simple","1slot");
+    ThreadVars *tv_detect1 = TmThreadCreate("Detect1","stream-queue1","simple","packetpool","packetpool","1slot", NULL, 0);
 //#endif
     //ThreadVars *tv_detect1 = TmThreadCreate("Detect1","decode-queue1","simple","alert-queue1","simple","1slot");
     if (tv_detect1 == NULL) {
@@ -637,12 +635,12 @@ int RunModeFilePcap(char *file) {
     }
     Tm1SlotSetFunc(tv_detect1,tm_module,(void *)g_de_ctx);
 
-    if (TmThreadSpawn(tv_detect1) != 0) {
+    if (TmThreadSpawn(tv_detect1, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_detect2 = TmThreadCreate("Detect2","stream-queue1","simple","alert-queue1","simple","1slot");
+    ThreadVars *tv_detect2 = TmThreadCreate("Detect2","stream-queue1","simple","packetpool","packetpool","1slot", NULL, 0);
     if (tv_detect2 == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -654,12 +652,12 @@ int RunModeFilePcap(char *file) {
     }
     Tm1SlotSetFunc(tv_detect2,tm_module,(void *)g_de_ctx);
 
-    if (TmThreadSpawn(tv_detect2) != 0) {
+    if (TmThreadSpawn(tv_detect2, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_alert = TmThreadCreate("AlertFastlog&Httplog","alert-queue1","simple","alert-queue2","simple","2slot");
+    ThreadVars *tv_alert = TmThreadCreate("AlertFastlog&Httplog","alert-queue1","simple","alert-queue2","simple","2slot", NULL, 0);
     if (tv_alert == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -678,12 +676,12 @@ int RunModeFilePcap(char *file) {
     }
     Tm2SlotSetFunc2(tv_alert,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_alert) != 0) {
+    if (TmThreadSpawn(tv_alert, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_unified = TmThreadCreate("AlertUnifiedLog","alert-queue2","simple","alert-queue3","simple","2slot");
+    ThreadVars *tv_unified = TmThreadCreate("AlertUnifiedLog","alert-queue2","simple","alert-queue3","simple","2slot", NULL, 0);
     if (tv_unified == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -703,12 +701,12 @@ int RunModeFilePcap(char *file) {
     }
     Tm2SlotSetFunc2(tv_unified,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_unified) != 0) {
+    if (TmThreadSpawn(tv_unified, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
 
-    ThreadVars *tv_debugalert = TmThreadCreate("AlertDebuglog","alert-queue3","simple","packetpool","packetpool","1slot");
+    ThreadVars *tv_debugalert = TmThreadCreate("AlertDebuglog","alert-queue3","simple","packetpool","packetpool","1slot", NULL, 0);
     if (tv_debugalert == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -720,7 +718,7 @@ int RunModeFilePcap(char *file) {
     }
     Tm1SlotSetFunc(tv_debugalert,tm_module,NULL);
 
-    if (TmThreadSpawn(tv_debugalert) != 0) {
+    if (TmThreadSpawn(tv_debugalert, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
@@ -735,7 +733,7 @@ int RunModeFilePcap2(char *file) {
     TimeModeSetOffline();
 
     /* create the threads */
-    ThreadVars *tv = TmThreadCreate("PcapFile","packetpool","packetpool","packetpool","packetpool","varslot");
+    ThreadVars *tv = TmThreadCreate("PcapFile","packetpool","packetpool","packetpool","packetpool","varslot", NULL, 0);
     if (tv == NULL) {
         printf("ERROR: TmThreadsCreate failed\n");
         exit(1);
@@ -804,7 +802,7 @@ int RunModeFilePcap2(char *file) {
     }
     TmVarSlotSetFuncAppend(tv,tm_module,NULL);
 
-    if (TmThreadSpawn(tv) != 0) {
+    if (TmThreadSpawn(tv, TVT_PPT, THV_USE | THV_PAUSE) != 0) {
         printf("ERROR: TmThreadSpawn failed\n");
         exit(1);
     }
@@ -814,7 +812,6 @@ int RunModeFilePcap2(char *file) {
 
 int main(int argc, char **argv)
 {
-    int rc;
     sigset_t set;
 
     sigaddset(&set, SIGINT); 
@@ -919,10 +916,6 @@ int main(int argc, char **argv)
 
     FlowInitConfig(FLOW_VERBOSE);
 
-    /* Initialize and set thread detached attribute */
-    pthread_attr_init(&attr);
-    pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
-
     SigLoadSignatures();
 
     struct timeval start_time;
@@ -934,34 +927,18 @@ int main(int argc, char **argv)
     RunModeFilePcap(argv[1]);
     //RunModeFilePcap2(argv[1]);
 
-    ThreadVars tv_flowmgr;
-    memset(&tv_flowmgr, 0, sizeof(ThreadVars));
-    printf("Creating FlowManagerThread...\n");
-    tv_flowmgr.name = "FlowManagerThread";
+    /* Spawn the flow manager thread */
+    FlowManagerThreadSpawn();
 
-    rc = pthread_create(&tv_flowmgr.t, &attr, FlowManagerThread, (void *)&tv_flowmgr);
-    if (rc) {
-        printf("ERROR; return code from pthread_create() is %d\n", rc);
-        exit(1);
-    }
-    TmThreadAppend(&tv_flowmgr);
+    /* Spawn the L7 App Detect thread */
+    L7AppDetectThreadSpawn();
 
-#include "l7-app-detect.h"
-    ThreadVars tv_l7appdetect;
-    memset(&tv_l7appdetect, 0, sizeof(ThreadVars));
-    printf("Creating L7 Application layer detect thread (WIP)...\n");
-    tv_l7appdetect.name = "L7AppDetectThread";
-
-    rc = pthread_create(&tv_l7appdetect.t, &attr, L7AppDetectThread, (void *)&tv_l7appdetect);
-    if (rc) {
-        printf("ERROR; return code from pthread_create() is %d\n", rc);
-        exit(1);
-    }
-    TmThreadAppend(&tv_l7appdetect);
-
-    printf("Creating Stats threads...\n");
+    /* Spawn the perf counter threads */
     PerfSpawnThreads();
 
+    /* Un-pause all the paused threads */
+    TmThreadContinueThreads();
+
     while(1) {
         if (sigflags) {
             printf("signal received\n");
@@ -998,8 +975,9 @@ int main(int argc, char **argv)
 
             printf("time elapsed %lus\n", end_time.tv_sec - start_time.tv_sec);
 
-            PerfReleaseResources();
             TmThreadKillThreads();
+
+            PerfReleaseResources();
 #if 0
 #ifdef DBG_PERF
             printf("th_v[0].nfq_t->dbg_maxreadsize %d\n", th_v[0].nfq_t->dbg_maxreadsize);
diff --git a/src/flow.c b/src/flow.c
index 03dd7aa5d4..301dd95662 100644
--- a/src/flow.c
+++ b/src/flow.c
@@ -4,6 +4,9 @@
 #include "debug.h"
 #include "decode.h"
 #include "threads.h"
+#include "tm-modules.h"
+#include "threadvars.h"
+#include "tm-threads.h"
 
 #include "util-time.h"
 
@@ -415,6 +418,8 @@ void *FlowManagerThread(void *td)
 
     while (1)
     {
+        TmThreadTestThreadUnPaused(th_v);
+
         if (sleeping >= 100 || flow_flags & FLOW_EMERGENCY)
         {
             u_int32_t timeout_new = flow_config.timeout_new;
@@ -474,3 +479,22 @@ void *FlowManagerThread(void *td)
     pthread_exit((void *) 0);
 }
 
+void FlowManagerThreadSpawn()
+{
+    ThreadVars *tv_flowmgr = NULL;
+
+    tv_flowmgr = TmThreadCreate("FlowManagerThread", NULL, NULL, NULL, NULL,
+                                "custom", FlowManagerThread, 0);
+    if (tv_flowmgr == NULL) {
+        printf("ERROR: TmThreadsCreate failed\n");
+        exit(1);
+    }
+    if (TmThreadSpawn(tv_flowmgr, TVT_PPT, THV_USE) != 0) {
+        printf("ERROR: TmThreadSpawn failed\n");
+        exit(1);
+    }
+
+    printf("Flow Manager thread spawned\n");
+
+    return;
+}
diff --git a/src/flow.h b/src/flow.h
index a2a0201c83..bf931920c5 100644
--- a/src/flow.h
+++ b/src/flow.h
@@ -93,5 +93,7 @@ void FlowDecrUsecnt(ThreadVars *, Packet *);
 
 void *FlowManagerThread(void *td);
 
+void FlowManagerThreadSpawn(void);
+
 #endif /* __FLOW_H__ */
 
diff --git a/src/l7-app-detect.c b/src/l7-app-detect.c
index 09ebb7d3c0..6aaed2b187 100644
--- a/src/l7-app-detect.c
+++ b/src/l7-app-detect.c
@@ -4,6 +4,9 @@
 #include "debug.h"
 #include "decode.h"
 #include "threads.h"
+#include "tm-modules.h"
+#include "threadvars.h"
+#include "tm-threads.h"
 
 #include "util-print.h"
 #include "util-pool.h"
@@ -68,6 +71,8 @@ void *L7AppDetectThread(void *td)
 
     /* main loop */
     while(run) {
+        TmThreadTestThreadUnPaused(tv);
+
         /* grab a msg, can return NULL on signals */
         StreamMsg *smsg = StreamMsgGetFromQueue(stream_q);
         if (smsg != NULL) {
@@ -133,3 +138,22 @@ void *L7AppDetectThread(void *td)
     pthread_exit((void *) 0);
 }
 
+void L7AppDetectThreadSpawn()
+{
+    ThreadVars *tv_l7appdetect = NULL;
+
+    tv_l7appdetect = TmThreadCreate("L7AppDetectThread", NULL, NULL, NULL, NULL,
+                                    "custom", L7AppDetectThread, 0);
+    if (tv_l7appdetect == NULL) {
+        printf("ERROR: TmThreadsCreate failed\n");
+        exit(1);
+    }
+    if (TmThreadSpawn(tv_l7appdetect, TVT_PPT, THV_USE) != 0) {
+        printf("ERROR: TmThreadSpawn failed\n");
+        exit(1);
+    }
+
+    printf("L7_App_Detect thread created\n");
+
+    return;
+}
diff --git a/src/l7-app-detect.h b/src/l7-app-detect.h
index 102cd88a14..1ff50951ac 100644
--- a/src/l7-app-detect.h
+++ b/src/l7-app-detect.h
@@ -3,4 +3,6 @@
 
 void *L7AppDetectThread(void *td);
 
+void L7AppDetectThreadSpawn(void);
+
 #endif /* __L7_APP_DETECT_H__ */
diff --git a/src/threadvars.h b/src/threadvars.h
index e5475617de..7b45adbec1 100644
--- a/src/threadvars.h
+++ b/src/threadvars.h
@@ -9,8 +9,9 @@
 
 /** Thread flags set and read by threads to control the threads */
 #define THV_USE     0x01 /** thread is in use */
-#define THV_KILL    0x02 /** thread should stop and prepare tp get joined. */
-#define THV_CLOSED  0x04 /** thread done, should be joinable */
+#define THV_PAUSE   0x02
+#define THV_KILL    0x04
+#define THV_CLOSED  0x08 /* thread done, should be joinable */
 
 /** \brief Per thread variable structure */
 typedef struct ThreadVars_ {
@@ -36,6 +37,9 @@ typedef struct ThreadVars_ {
     PerfContext pctx;
     PerfCounterArray *pca;
 
+    pthread_mutex_t *m;
+    pthread_cond_t *cond;
+
     struct ThreadVars_ *next;
     struct ThreadVars_ *prev;
 } ThreadVars;
diff --git a/src/tm-threads.c b/src/tm-threads.c
index db6b6f4f89..2a551f9c04 100644
--- a/src/tm-threads.c
+++ b/src/tm-threads.c
@@ -1,4 +1,6 @@
-/* Copyright (c) 2008 Victor Julien <victor@inliniac.net> */
+/** Copyright (c) 2009 Open Information Security Foundation.
+ *  \author Victor Julien <victor@inliniac.net>
+ */
 
 #include <sys/types.h> /* for gettid(2) */
 #define _GNU_SOURCE
@@ -11,13 +13,16 @@
 #include "tm-queues.h"
 #include "tm-queuehandlers.h"
 #include "tm-modules.h"
+#include "tm-threads.h"
 
 /* prototypes */
 static int SetCPUAffinity(int cpu);
 
-
 /* root of the threadvars list */
-ThreadVars *tv_root = NULL;
+ThreadVars *tv_root[TVT_MAX] = { NULL };
+
+/* lock to protect tv_root */
+pthread_mutex_t tv_root_lock = PTHREAD_MUTEX_INITIALIZER;
 
 typedef struct TmSlot_ {
     /* function pointers */
@@ -79,6 +84,8 @@ void *TmThreadsSlot1NoIn(void *td) {
     memset(&s->s.slot_pq, 0, sizeof(PacketQueue));
 
     while(run) {
+        TmThreadTestThreadUnPaused(tv);
+
         r = s->s.SlotFunc(tv, p, s->s.slot_data, &s->s.slot_pq);
         while (s->s.slot_pq.len > 0) {
             Packet *extra = PacketDequeue(&s->s.slot_pq);
@@ -134,6 +141,8 @@ void *TmThreadsSlot1NoOut(void *td) {
     memset(&s->s.slot_pq, 0, sizeof(PacketQueue));
 
     while(run) {
+        TmThreadTestThreadUnPaused(tv);
+
         p = tv->tmqh_in(tv);
 
         r = s->s.SlotFunc(tv, p, s->s.slot_data, /* no outqh no pq */NULL);
@@ -185,6 +194,8 @@ void *TmThreadsSlot1NoInOut(void *td) {
     memset(&s->s.slot_pq, 0, sizeof(PacketQueue));
 
     while(run) {
+        TmThreadTestThreadUnPaused(tv);
+
         r = s->s.SlotFunc(tv, NULL, s->s.slot_data, /* no outqh, no pq */NULL);
         //printf("%s: TmThreadsSlot1NoInNoOut: r %d\n", tv->name, r);
         /* XXX handle error */
@@ -239,6 +250,8 @@ void *TmThreadsSlot1(void *td) {
     memset(&s->s.slot_pq, 0, sizeof(PacketQueue));
 
     while(run) {
+        TmThreadTestThreadUnPaused(tv);
+
         /* input a packet */
         p = tv->tmqh_in(tv);
 
@@ -317,6 +330,8 @@ void *TmThreadsSlot2(void *td) {
     }
 
     while(run) {
+        TmThreadTestThreadUnPaused(tv);
+
         /* input a packet */
         p = tv->tmqh_in(tv);
 
@@ -437,6 +452,8 @@ void *TmThreadsSlot3(void *td) {
     }
 
     while(run) {
+        TmThreadTestThreadUnPaused(tv);
+
         /* input a packet */
         p = tv->tmqh_in(tv);
 
@@ -618,6 +635,8 @@ void *TmThreadsSlotVar(void *td) {
     }
 
     while(run) {
+        TmThreadTestThreadUnPaused(tv);
+
         /* input a packet */
         p = tv->tmqh_in(tv);
         //printf("TmThreadsSlotVar: %p\n", p);
@@ -661,9 +680,19 @@ void *TmThreadsSlotVar(void *td) {
     pthread_exit((void *) 0);
 }
 
-int TmThreadSetSlots(ThreadVars *tv, char *name) {
+int TmThreadSetSlots(ThreadVars *tv, char *name, void *(*fn_p)(void *)) {
     u_int16_t size = 0;
 
+    if (name == NULL) {
+        if (fn_p == NULL) {
+            printf("Both slot name and function pointer can't be NULL inside "
+                   "TmThreadSetSlots\n");
+            goto error;
+        }
+        else
+            name = "custom";
+    }
+
     if (strcmp(name, "1slot") == 0) {
         size = sizeof(Tm1Slot);
         tv->tm_func = TmThreadsSlot1;
@@ -685,6 +714,12 @@ int TmThreadSetSlots(ThreadVars *tv, char *name) {
     } else if (strcmp(name, "varslot") == 0) {
         size = sizeof(TmVarSlot);
         tv->tm_func = TmThreadsSlotVar;
+    } else if (strcmp(name, "custom") == 0) {
+        if (fn_p == NULL)
+            goto error;
+
+        tv->tm_func = fn_p;
+        return 0;
     }
 
     tv->tm_slots = malloc(size);
@@ -835,7 +870,25 @@ int TmThreadSetCPUAffinity(ThreadVars *tv, int cpu) {
     return 0;
 }
 
-ThreadVars *TmThreadCreate(char *name, char *inq_name, char *inqh_name, char *outq_name, char *outqh_name, char *slots) {
+/**
+ * \brief Creates and returns the TV instance for a new thread.
+ *
+ * \param name       Name of this TV instance
+ * \param inq_name   Incoming queue name
+ * \param inqh_name  Incoming queue handler name as set by TmqhSetup()
+ * \param outq_name  Outgoing queue name
+ * \param outqh_name Outgoing queue handler as set by TmqhSetup()
+ * \param slots      String representation for the slot function to be used
+ * \param fn_p       Pointer to function when \"slots\" is of type \"custom\"
+ * \param mucond     Flag to indicate whether to initialize the condition
+ *                   and the mutex variables for this newly created TV.
+ *
+ * \retval the newly created TV instance, or NULL on error
+ */
+ThreadVars *TmThreadCreate(char *name, char *inq_name, char *inqh_name,
+                           char *outq_name, char *outqh_name, char *slots,
+                           void * (*fn_p)(void *), int mucond)
+{
     ThreadVars *tv = NULL;
     Tmq *tmq = NULL;
     Tmqh *tmqh = NULL;
@@ -889,19 +942,28 @@ ThreadVars *TmThreadCreate(char *name, char *inq_name, char *inqh_name, char *ou
         //printf("TmThreadCreate: tv->tmqh_out %p\n", tv->tmqh_out);
     }
 
-    if (TmThreadSetSlots(tv, slots) != 0) {
+    if (TmThreadSetSlots(tv, slots, fn_p) != 0) {
         goto error;
     }
 
+    if (mucond != 0)
+        TmThreadInitMC(tv);
+
     return tv;
 error:
     printf("ERROR: failed to setup a thread.\n");
     return NULL;
 }
 
-void TmThreadAppend(ThreadVars *tv) {
-    if (tv_root == NULL) {
-        tv_root = tv;
+/**
+ * \brief Appends this TV to tv_root based on its type
+ *
+ * \param type holds the type this TV belongs to.
+ */
+void TmThreadAppend(ThreadVars *tv, int type)
+{
+    if (tv_root[type] == NULL) {
+        tv_root[type] = tv;
         tv->next = NULL;
         tv->prev = NULL;
 
@@ -909,7 +971,7 @@ void TmThreadAppend(ThreadVars *tv) {
         return;
     }
 
-    ThreadVars *t = tv_root;
+    ThreadVars *t = tv_root[type];
 
     while (t) {
         if (t->next == NULL) {
@@ -926,62 +988,102 @@ void TmThreadAppend(ThreadVars *tv) {
 }
 
 void TmThreadKillThreads(void) {
-    ThreadVars *t = tv_root;
+    ThreadVars *t = NULL;
+    int i = 0;
 
-    while (t) {
-        t->flags |= THV_KILL;
-        //printf("TmThreadKillThreads: told thread %s to stop\n", t->name);
+    for (i = 0; i < TVT_MAX; i++) {
+        t = tv_root[i];
 
-        /* XXX hack */
-        StreamMsgSignalQueueHack();
 
-        if (t->inq != NULL) {
-            int i;
+        while (t) {
+            t->flags |= THV_KILL;
+            printf("TmThreadKillThreads: told thread %s to stop\n", t->name);
 
-            //printf("TmThreadKillThreads: t->inq->usecnt %u\n", t->inq->usecnt);
+            /* XXX hack */
+            StreamMsgSignalQueueHack();
 
-            /* make sure our packet pending counter doesn't block */
-            pthread_cond_signal(&cond_pending);
+            if (t->inq != NULL) {
+                int i;
 
-            /* signal the queue for the number of users */
-            for (i = 0; i < t->inq->usecnt; i++)
-                pthread_cond_signal(&trans_q[t->inq->id].cond_q);
+                //printf("TmThreadKillThreads: t->inq->usecnt %u\n", t->inq->usecnt);
 
-            /* to be sure, signal more */
-            int cnt = 0;
-            while (1) {
-                if (t->flags & THV_CLOSED) {
-                    //printf("signalled the thread %d times\n", cnt);
-                    break;
-                }
+                /* make sure our packet pending counter doesn't block */
+                pthread_cond_signal(&cond_pending);
 
-                cnt++;
+                /* signal the queue for the number of users */
 
                 for (i = 0; i < t->inq->usecnt; i++)
                     pthread_cond_signal(&trans_q[t->inq->id].cond_q);
 
-                usleep(100);
+                /* to be sure, signal more */
+                int cnt = 0;
+                while (1) {
+                    if (t->flags & THV_CLOSED) {
+                        printf("signalled the thread %d times\n", cnt);
+                        break;
+                    }
+
+                    cnt++;
+
+                    for (i = 0; i < t->inq->usecnt; i++)
+                        pthread_cond_signal(&trans_q[t->inq->id].cond_q);
+
+                    usleep(100);
+                }
+
+                printf("TmThreadKillThreads: signalled t->inq->id %u\n", t->inq->id);
+
             }
 
-            //printf("TmThreadKillThreads: signalled t->inq->id %u\n", t->inq->id);
-        }
+            if (t->cond != NULL ) {
+                int cnt = 0;
+                while (1) {
+                    if (t->flags & THV_CLOSED) {
+                        printf("signalled the thread %d times\n", cnt);
+                        break;
+                    }
 
-        /* join it */
-        pthread_join(t->t, NULL);
-        printf("TmThreadKillThreads: thread %s stopped\n", t->name);
+                    cnt++;
 
-        t = t->next;
+                    pthread_cond_broadcast(t->cond);
+
+                    usleep(100);
+                }
+            }
+
+            /* join it */
+            pthread_join(t->t, NULL);
+            printf("TmThreadKillThreads: thread %s stopped\n", t->name);
+
+            t = t->next;
+        }
     }
 }
 
-int TmThreadSpawn(ThreadVars *tv) {
+/**
+ * \brief Spawns a thread associated with the ThreadVars instance tv
+ *
+ * \param type  Type this TV belongs to.
+ * \param flags Flags that should be set for this thread
+ *
+ * \retval 0 on success and -1 on failure
+ */
+int TmThreadSpawn(ThreadVars *tv, int type, int flags)
+{
     pthread_attr_t attr;
 
+    if (type < 0 || type >= TVT_MAX) {
+        printf("ThreadVars of category %d does not exist\n", type);
+        return -1;
+    }
+
     if (tv->tm_func == NULL) {
         printf("ERROR: no thread function set\n");
         return -1;
     }
 
+    tv->flags = flags;
+
     /* Initialize and set thread detached attribute */
     pthread_attr_init(&attr);
     pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
@@ -992,8 +1094,116 @@ int TmThreadSpawn(ThreadVars *tv) {
         return -1;
     }
 
-    TmThreadAppend(tv);
+    TmThreadAppend(tv, type);
 
     return 0;
 }
 
+/**
+ * \brief Initializes the mutex and condition variables for this TV
+ *
+ * \param tv Pointer to a TV instance
+ */
+void TmThreadInitMC(ThreadVars *tv)
+{
+    if ( (tv->m = malloc(sizeof(pthread_mutex_t))) == NULL) {
+        printf("Error allocating memory\n");
+        exit(0);
+    }
+
+    if (pthread_mutex_init(tv->m, NULL) != 0) {
+        printf("Error initializing the tv->m mutex\n");
+        exit(0);
+    }
+
+    if ( (tv->cond = malloc(sizeof(pthread_cond_t))) == NULL) {
+        printf("Error allocating memory\n");
+        exit(0);
+    }
+
+    if (pthread_cond_init(tv->cond, NULL) != 0) {
+        printf("Error initializing the tv->cond condition variable\n");
+        exit(0);
+    }
+}
+
+/**
+ * \brief Tests if the thread represented in the arg has been unpaused or not.
+ *
+ *        The function would return if the thread tv has been unpaused or if the
+ *        kill flag for the thread has been set.
+ *
+ * \param tv Pointer to the TV instance.
+ */
+void TmThreadTestThreadUnPaused(ThreadVars *tv)
+{
+    while (tv->flags & THV_PAUSE) {
+        usleep(100);
+        if (tv->flags & THV_KILL)
+            break;
+    }
+
+    return;
+}
+
+/**
+ * \brief Unpauses a thread
+ *
+ * \param tv Pointer to a TV instance that has to be unpaused
+ */
+void TmThreadContinue(ThreadVars *tv)
+{
+    tv->flags &= ~THV_PAUSE;
+
+    return;
+}
+
+/**
+ * \brief Unpauses all threads present in tv_root
+ */
+void TmThreadContinueThreads()
+{
+    ThreadVars *tv = NULL;
+    int i = 0;
+
+    for (i = 0; i < TVT_MAX; i++) {
+        tv = tv_root[i];
+        while (tv != NULL) {
+            TmThreadContinue(tv);
+            tv = tv->next;
+        }
+    }
+
+    return;
+}
+
+/**
+ * \brief Pauses a thread
+ *
+ * \param tv Pointer to a TV instance that has to be paused
+ */
+void TmThreadPause(ThreadVars *tv)
+{
+    tv->flags |= THV_PAUSE;
+
+    return;
+}
+
+/**
+ * \brief Pauses all threads present in tv_root
+ */
+void TmThreadPauseThreads()
+{
+    ThreadVars *tv = NULL;
+    int i = 0;
+
+    for (i = 0; i < TVT_MAX; i++) {
+        tv = tv_root[i];
+        while (tv != NULL) {
+            TmThreadPause(tv);
+            tv = tv->next;
+        }
+    }
+
+    return;
+}
diff --git a/src/tm-threads.h b/src/tm-threads.h
index 202b3b0b96..1cefe448d2 100644
--- a/src/tm-threads.h
+++ b/src/tm-threads.h
@@ -1,20 +1,55 @@
 #ifndef __TM_THREADS_H__
 #define __TM_THREADS_H__
 
-extern ThreadVars *tv_root;
+/* ThreadVars type */
+enum {
+    TVT_PPT,
+    TVT_MGMT,
+    TVT_MAX,
+};
+
+extern ThreadVars *tv_root[TVT_MAX];
+
+extern pthread_mutex_t tv_root_lock;
 
 void Tm1SlotSetFunc(ThreadVars *, TmModule *, void *);
+
 void Tm2SlotSetFunc1(ThreadVars *, TmModule *, void *);
+
 void Tm2SlotSetFunc2(ThreadVars *, TmModule *, void *);
+
 void Tm3SlotSetFunc1(ThreadVars *, TmModule *, void *);
+
 void Tm3SlotSetFunc2(ThreadVars *, TmModule *, void *);
+
 void Tm3SlotSetFunc3(ThreadVars *, TmModule *, void *);
+
 void TmVarSlotSetFuncAppend(ThreadVars *, TmModule *, void *);
-ThreadVars *TmThreadCreate(char *name, char *inq_name, char *inqh_name, char *outq_name, char *outqh_name, char *slots);
-int TmThreadSpawn(ThreadVars *);
+
+
+ThreadVars *TmThreadCreate(char *name, char *inq_name, char *inqh_name,
+                           char *outq_name, char *outqh_name, char *slots,
+                           void *(fn_p)(void *), int);
+
+int TmThreadSpawn(ThreadVars *, int, int);
+
 void TmThreadKillThreads(void);
-void TmThreadAppend(ThreadVars *);
+
+void TmThreadAppend(ThreadVars *, int);
+
 int TmThreadSetCPUAffinity(ThreadVars *, int);
 
+void TmThreadInitMC(ThreadVars *);
+
+void TmThreadTestThreadUnPaused(ThreadVars *);
+
+void TmThreadContinue(ThreadVars *);
+
+void TmThreadContinueThreads(void);
+
+void TmThreadPause(ThreadVars *);
+
+void TmThreadPauseThreads(void);
+
 #endif /* __TM_THREADS_H__ */