Index: firmware/App/Modes/FlushPermeate.c
===================================================================
diff -u -r6dd382e3988fac2f9ee041b4738d67305e17a6a2 -r2652d50bbc5e78ed6fe3ad9ccbca0be6f802f1ff
--- firmware/App/Modes/FlushPermeate.c	(.../FlushPermeate.c)	(revision 6dd382e3988fac2f9ee041b4738d67305e17a6a2)
+++ firmware/App/Modes/FlushPermeate.c	(.../FlushPermeate.c)	(revision 2652d50bbc5e78ed6fe3ad9ccbca0be6f802f1ff)
@@ -134,8 +134,8 @@
 /*********************************************************************//**
  * @brief
  * The handlePermeateFlushProgressState handles the in progress state of Permeate flush
- * @details \b Inputs:  none
- * @details \b Outputs: none
+ * @details \b Inputs:  permeateFlushTimer, permeateFlushAlarmTimer
+ * @details \b Outputs: isFlushComplete
  * @return the next state of Permeate flush state
  *************************************************************************/
 static FP_PERM_FLUSH_STATE_T handlePermeateFlushProgressState( void )
@@ -167,14 +167,15 @@
         }
 
     }
+
     return state;
 }
 
 /*********************************************************************//**
  * @brief
  * The handlePermeateFlushProgressState handles the in progress state of Permeate flush
- * @details \b Inputs:  none
- * @details \b Outputs: none
+ * @details \b Inputs:  pendingStartPermeateFlushRequest
+ * @details \b Outputs: isFlushComplete
  * @return the next state of Permeate flush state
  *************************************************************************/
 static FP_PERM_FLUSH_STATE_T handlePermeateFlushPausedState( void )
@@ -186,6 +187,7 @@
         isFlushComplete = FALSE;
         state = PERM_FLUSH_IN_PROGRESS;
     }
+
     return state;
 }
 
@@ -195,6 +197,7 @@
  * for the state transition in Permeate flush mode.
  * @details Inputs: Valve states, Pump speed
  * @details Outputs: Actuate valves, pumps as desired.
+ * @details \b Alarm: ALARM_ID_FP_SOFTWARE_FAULT if in invalid flush transition
  * @param state Permeate flush state enum
  * @return none
  *************************************************************************/
@@ -260,7 +263,7 @@
  * The signalStartPermeateFlush function signals the FP to start Permeate flush.
  * @details \b Inputs: none
  * @details \b Outputs: pendingStartPermeateFlushRequest
- * @return the current state of Permeate flush
+ * @return none
  *************************************************************************/
 void signalStartPermeateFlush( void )
 {
@@ -289,7 +292,7 @@
  * The getCurrentPermeateFlushState function returns the current state of
  * Permeate flush.
  * @details \b Inputs: permeateFlushState
- * @details \b Outputs: permeateFlushState
+ * @details \b Outputs: none
  * @return the current state of Permeate flush
  *************************************************************************/
 FP_PERM_FLUSH_STATE_T getCurrentPermeateFlushState( void )
@@ -299,10 +302,11 @@
 
 /*********************************************************************//**
  * @brief
- * The isPermeateFlushComplete function returns isPermeateFlushComplete.
- * @details \b Inputs: none
+ * The isPermeateFlushComplete function returns the state of completeness
+ * of Permeate Flush.
+ * @details \b Inputs: isFlushComplete
  * @details \b Outputs: none
- * @return the complete boolean for Permeate flush.
+ * @return TRUE if permeate flush is complete, FALSE if not.
  *************************************************************************/
 BOOL isPermeateFlushComplete( void )
 {