Index: trunk/ippTools/src/chiptool.c
===================================================================
--- trunk/ippTools/src/chiptool.c	(revision 25793)
+++ trunk/ippTools/src/chiptool.c	(revision 25800)
@@ -728,12 +728,23 @@
     PXOPT_COPY_S64(config->args, where, "-chip_id", "chip_id", "==");
     PXOPT_COPY_STR(config->args, where, "-class_id", "class_id", "==");
-    PXOPT_LOOKUP_S16(fault, config->args, "-fault", true, false);
-
-    if (!pxSetFaultCode(config->dbh, "chipProcessedImfile", where, fault)) {
+    PXOPT_LOOKUP_STR(state, config->args, "-set_state", false, NULL);
+        
+    if (!state) {
+      PXOPT_LOOKUP_S16(fault, config->args, "-fault", true, false);
+      
+      if (!pxSetFaultCode(config->dbh, "chipProcessedImfile", where, fault)) {
         psError(PS_ERR_UNKNOWN, false, "failed to set set fault flag");
         return false;
-    }
-    psFree(where);
-
+      }
+      psFree(where);
+    }
+    else {
+      if (!pxchipProcessedImfileSetStateByQuery(config,where,state)) {
+	psError(PS_ERR_UNKNOWN, false, "failed to set chipProcessedImfile state");
+	return(false);
+      }
+    }
+
+      
     return true;
 }
Index: trunk/ippTools/src/chiptoolConfig.c
===================================================================
--- trunk/ippTools/src/chiptoolConfig.c	(revision 25793)
+++ trunk/ippTools/src/chiptoolConfig.c	(revision 25800)
@@ -182,5 +182,5 @@
     psMetadataAddStr(updateprocessedimfileArgs,  PS_LIST_TAIL, "-class_id",           0, "search by class ID", NULL);
     psMetadataAddS16(updateprocessedimfileArgs, PS_LIST_TAIL, "-fault",  0,            "set fault code (required)", 0);
-
+    psMetadataAddStr(updateprocessedimfileArgs, PS_LIST_TAIL, "-set_state", 0,         "set state", NULL);
     // -block
     psMetadata *blockArgs = psMetadataAlloc();
Index: trunk/ippTools/src/difftool.c
===================================================================
--- trunk/ippTools/src/difftool.c	(revision 25793)
+++ trunk/ippTools/src/difftool.c	(revision 25800)
@@ -51,4 +51,11 @@
 
 static bool setdiffRunState(pxConfig *config, psS64 diff_id, const char *state, psS64 magicked);
+static bool setdiffRunStateByLabel(pxConfig *config, const char* label, const char *state);
+static bool change_skyfile_data_state(pxConfig *config, psString data_state, psString run_state);
+static bool tocleanedskyfileMode(pxConfig *config);
+static bool topurgedskyfileMode(pxConfig *config);
+static bool toscrubbedskyfileMode(pxConfig *config);
+
+
 
 # define MODECASE(caseName, func) \
@@ -88,4 +95,8 @@
         MODECASE(DIFFTOOL_MODE_EXPORTRUN,             exportrunMode);
         MODECASE(DIFFTOOL_MODE_IMPORTRUN,             importrunMode);
+        MODECASE(DIFFTOOL_MODE_TOCLEANEDSKYFILE,   tocleanedskyfileMode);
+	MODECASE(DIFFTOOL_MODE_TOPURGEDSKYFILE,    topurgedskyfileMode);
+	MODECASE(DIFFTOOL_MODE_TOSCRUBBEDSKYFILE,  toscrubbedskyfileMode);
+
         default:
             psAbort("invalid option (this should not happen)");
@@ -169,13 +180,21 @@
 
     // required options
-    PXOPT_LOOKUP_S64(diff_id, config->args, "-diff_id", true, false);
+    PXOPT_LOOKUP_S64(diff_id, config->args, "-diff_id", false, false);
     PXOPT_LOOKUP_STR(state, config->args, "-state", true, false);
-
-    if (state) {
+    PXOPT_LOOKUP_STR(label, config->args, "-label", false, false);
+    
+    // Copy of my hacky work around from stacktool.c
+    if ((state)&&(diff_id)) {
         // set detRun.state to state
         return setdiffRunState(config, diff_id, state, false);
     }
 
-    return true;
+    if ((state)&&(label)) {
+      return setdiffRunStateByLabel(config, label, state);
+    }
+
+    psError(PS_ERR_UNKNOWN, false, "Required options not found.");
+
+    return false;
 }
 
@@ -865,13 +884,44 @@
     }
 
-    char *query = "UPDATE diffRun SET state = '%s', magicked = %" PRId64 " WHERE diff_id = %"PRId64;
-
-    if (!p_psDBRunQueryF(config->dbh, query, state, magicked, diff_id)) {
+    if (magicked) {
+      char *query = "UPDATE diffRun SET state = '%s', magicked = %" PRId64 " WHERE diff_id = %"PRId64;
+      
+      if (!p_psDBRunQueryF(config->dbh, query, state, magicked, diff_id)) {
         psError(PS_ERR_UNKNOWN, false,
                 "failed to change state for diff_id %"PRId64, diff_id);
         return false;
-    }
-
+      }
+    }
+    else {
+      char *query = "UPDATE diffRun SET state = '%s' WHERE diff_id = %"PRId64;
+      
+      if (!p_psDBRunQueryF(config->dbh, query, state, diff_id)) {
+        psError(PS_ERR_UNKNOWN, false,
+                "failed to change state for diff_id %"PRId64, diff_id);
+        return false;
+      }
+    }
+    
     return true;
+}
+
+
+static bool setdiffRunStateByLabel(pxConfig *config, const char *label, const char *state) {
+  PS_ASSERT_PTR_NON_NULL(state,false);
+
+  // check that state is a valid string value
+  if (!pxIsValidState(state)) {
+    psError(PS_ERR_UNKNOWN, false, "invalid diffRun state: %s", state);
+    return false;
+  }
+
+  char *query = "UPDATE diffRun SET state = '%s' WHERE label = '%s'";
+  if (!p_psDBRunQueryF(config->dbh,query,state,label)) {
+    psError(PS_ERR_UNKNOWN, false,
+	    "failed to change state for label %s", label);
+    return(false);
+  }
+
+  return true;
 }
 
@@ -1725,5 +1775,5 @@
 
     psMetadata *where = psMetadataAlloc();
-    pxAddLabelSearchArgs (config, where, "-label", "diffRun.label", "==");
+    pxAddLabelSearchArgs (config, where, "-label", "label", "==");
 
     psString query = pxDataGet("difftool_pendingcleanuprun.sql");
@@ -1747,4 +1797,5 @@
     }
 
+    //    fprintf(stderr,"%s",query);
     if (!p_psDBRunQuery(config->dbh, query)) {
         psError(PS_ERR_UNKNOWN, false, "database error");
@@ -1918,4 +1969,59 @@
 
     return true;
+}
+
+static bool change_skyfile_data_state(pxConfig *config, psString data_state, psString run_state) {
+  PS_ASSERT_PTR_NON_NULL(config, false);
+
+  // diff_id, skycell_id are required
+  PXOPT_LOOKUP_S64(diff_id, config->args, "-diff_id", true, false);
+  PXOPT_LOOKUP_STR(skycell_id, config->args, "-skycell_id", true, false);
+
+  psString query = pxDataGet("difftool_change_skyfile_data_state.sql");
+
+  if (!psDBTransaction(config->dbh)) {
+    psError(PS_ERR_UNKNOWN, false, "database error");
+    return(false);
+  }
+
+  // Uses the unconstrained (diffRun.state [NEED NOT EQUAL] run_state) version from warptool.c
+
+  if (!p_psDBRunQueryF(config->dbh, query, data_state, diff_id, skycell_id)) {
+    psError(PS_ERR_UNKNOWN, false, "database error");
+    // rollback
+    if (!psDBRollback(config->dbh)) {
+      psError(PS_ERR_UNKNOWN, false, "database error");
+    }
+    psError(PS_ERR_UNKNOWN, false, "database error");
+    return(false);
+  }
+  psFree(query);
+
+  query = pxDataGet("difftool_change_run_state.sql");
+  if (!p_psDBRunQueryF(config->dbh, query, data_state, diff_id, data_state)) {
+    // rollback
+    if (!psDBRollback(config->dbh)) {
+      psError(PS_ERR_UNKNOWN, false, "database error");
+    }
+    psError(PS_ERR_UNKNOWN, false, "database error");
+    return(false);
+  }
+
+  if (!psDBCommit(config->dbh)) {
+    psError(PS_ERR_UNKNOWN, false, "database error");
+    return(false);
+  }
+  
+  return(true);
+}
+
+static bool tocleanedskyfileMode(pxConfig *config) {
+  return change_skyfile_data_state(config, "cleaned","goto_cleaned");
+}
+static bool topurgedskyfileMode(pxConfig *config) {
+  return change_skyfile_data_state(config, "purged", "goto_purged");
+}
+static bool toscrubbedskyfileMode(pxConfig *config) {
+  return change_skyfile_data_state(config, "scrubbed", "goto_scrubbed");
 }
 
Index: trunk/ippTools/src/difftool.h
===================================================================
--- trunk/ippTools/src/difftool.h	(revision 25793)
+++ trunk/ippTools/src/difftool.h	(revision 25800)
@@ -42,5 +42,9 @@
     DIFFTOOL_MODE_UPDATEDIFFSKYFILE,
     DIFFTOOL_MODE_EXPORTRUN,
-    DIFFTOOL_MODE_IMPORTRUN
+    DIFFTOOL_MODE_IMPORTRUN,
+    DIFFTOOL_MODE_TOCLEANEDSKYFILE,
+    DIFFTOOL_MODE_TOPURGEDSKYFILE,
+    DIFFTOOL_MODE_TOSCRUBBEDSKYFILE
+    
 } difftoolMode;
 
Index: trunk/ippTools/src/difftoolConfig.c
===================================================================
--- trunk/ippTools/src/difftoolConfig.c	(revision 25793)
+++ trunk/ippTools/src/difftoolConfig.c	(revision 25800)
@@ -60,5 +60,6 @@
     psMetadataAddS64(updaterunArgs, PS_LIST_TAIL, "-diff_id", 0,            "define diff ID (required)", 0);
     psMetadataAddStr(updaterunArgs, PS_LIST_TAIL, "-state", 0,            "set state (required)", NULL);
-
+    psMetadataAddStr(updaterunArgs, PS_LIST_TAIL, "-label", 0,            "define by label instead of diff ID", 0);
+    
     // -addinputskyfile
     psMetadata *addinputskyfileArgs = psMetadataAlloc();
@@ -258,4 +259,19 @@
     psMetadataAddS16(updatediffskyfileArgs, PS_LIST_TAIL, "-fault", 0,         "set fault code (required)", 0);
 
+    // -tocleanedskyfile
+    psMetadata *tocleanedskyfileArgs = psMetadataAlloc();
+    psMetadataAddS64(tocleanedskyfileArgs, PS_LIST_TAIL, "-diff_id", 0, "difftool ID to update", 0);
+    psMetadataAddStr(tocleanedskyfileArgs, PS_LIST_TAIL, "-skycell_id", 0, "skycell ID to update", NULL);
+
+    // -topurgedskyfile
+    psMetadata *topurgedskyfileArgs = psMetadataAlloc();
+    psMetadataAddS64(topurgedskyfileArgs, PS_LIST_TAIL, "-diff_id", 0,    "difftool ID to update", 0);
+    psMetadataAddStr(topurgedskyfileArgs, PS_LIST_TAIL, "-skycell_id", 0, "skycell ID to update", NULL);
+
+    // -toscrubbedskyfile
+    psMetadata *toscrubbedskyfileArgs = psMetadataAlloc();
+    psMetadataAddS64(toscrubbedskyfileArgs, PS_LIST_TAIL, "-diff_id", 0, "difftool ID to update", 0);
+    psMetadataAddStr(toscrubbedskyfileArgs, PS_LIST_TAIL, "-skycell_id", 0, "skycell ID to update", NULL);
+
     // -exportrun
     psMetadata *exportrunArgs = psMetadataAlloc();
@@ -295,4 +311,8 @@
     PXOPT_ADD_MODE("-importrun",            "import run from metadata file",           DIFFTOOL_MODE_IMPORTRUN, importrunArgs);
 
+    PXOPT_ADD_MODE("-tocleanedskyfile", "set skyfile as cleaned", DIFFTOOL_MODE_TOCLEANEDSKYFILE, tocleanedskyfileArgs);
+    PXOPT_ADD_MODE("-topurgedskyfile", "set skyfile as purged", DIFFTOOL_MODE_TOPURGEDSKYFILE, topurgedskyfileArgs);
+    PXOPT_ADD_MODE("-toscrubbedskyfile", "set skyfile as scrubbed", DIFFTOOL_MODE_TOSCRUBBEDSKYFILE, toscrubbedskyfileArgs);
+    
     if (!pxGetOptions(stderr, argc, argv, config, modes, argSets)) {
         psError(PS_ERR_UNKNOWN, true, "option parsing failed");
Index: trunk/ippTools/src/pxchip.c
===================================================================
--- trunk/ippTools/src/pxchip.c	(revision 25793)
+++ trunk/ippTools/src/pxchip.c	(revision 25800)
@@ -192,5 +192,4 @@
 }
 
-
 bool pxchipRunSetLabel(pxConfig *config, psS64 chip_id, const char *label)
 {
@@ -233,4 +232,43 @@
 }
 
+bool pxchipProcessedImfileSetStateByQuery(pxConfig *config, psMetadata *where, const char *state)
+{
+    PS_ASSERT_PTR_NON_NULL(config, false);
+    PS_ASSERT_PTR_NON_NULL(state, false);
+
+    // check that state is a valid string value
+    if (!pxIsValidState(state)) {
+        psError(PS_ERR_UNKNOWN, false, "invalid chipProcessedImfile state: %s", state);
+        return false;
+    }
+
+/*     if (!strcmp(state, "full")) { */
+/*         // There are states that need to be met for a run to be set to full that we don't */
+/*         // check here. */
+/*         // for example all of the run's Imfiles must have chipProcessedImfile.data_state == "full" */
+/*         // chipRun.magicked = (SUM(!chipProcessedImfile.magicked) = 0) */
+/*         // so don't do allow setting the state to full */
+/*         psError(PS_ERR_UNKNOWN, true, "cannot use -updaterun so set chipRun state to full"); */
+/*         return false; */
+/*     } */
+
+    psString query = psStringCopy("UPDATE chipProcessedImfile JOIN chipRun USING(chip_id) JOIN rawExp ON chipRun.exp_id = rawExp.exp_id SET state = '%s'");
+
+    if (where && psListLength(where->list) > 0) {
+        psString whereClause = psDBGenerateWhereSQL(where, NULL);
+        psStringAppend(&query, " %s", whereClause);
+        psFree(whereClause);
+    }
+
+    if (!p_psDBRunQueryF(config->dbh, query, state)) {
+        psFree(query);
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        return false;
+    }
+
+    psFree(query);
+
+    return true;
+}
 
 psS64 pxchipQueueByExpTag(pxConfig *config,
Index: trunk/ippTools/src/pxchip.h
===================================================================
--- trunk/ippTools/src/pxchip.h	(revision 25793)
+++ trunk/ippTools/src/pxchip.h	(revision 25800)
@@ -25,8 +25,12 @@
 #include "pxtools.h"
 
+
+
 bool pxchipRunSetState(pxConfig *config, psS64 chip_id, const char *state, const bool magicked);
 bool pxchipRunSetStateByQuery(pxConfig *config, psMetadata *where, const char *state);
 bool pxchipRunSetLabel(pxConfig *config, psS64 chip_id, const char *label);
 bool pxchipRunSetLabelByQuery(pxConfig *config, psMetadata *where, const char *label);
+
+bool pxchipProcessedImfileSetStateByQuery(pxConfig *config, psMetadata *where, const char *state);
 
 psS64 pxchipQueueByExpTag(pxConfig *config,
Index: trunk/ippTools/src/stacktool.c
===================================================================
--- trunk/ippTools/src/stacktool.c	(revision 25793)
+++ trunk/ippTools/src/stacktool.c	(revision 25800)
@@ -48,4 +48,5 @@
 
 static bool setstackRunState(pxConfig *config, psS64 stack_id, const char *state);
+static bool setstackRunStateByLabel(pxConfig *config, const char *label, const char *state);
 
 # define MODECASE(caseName, func) \
@@ -569,13 +570,21 @@
     PS_ASSERT_PTR_NON_NULL(config, false);
 
-    PXOPT_LOOKUP_S64(stack_id, config->args, "-stack_id", true, false);
+    PXOPT_LOOKUP_S64(stack_id, config->args, "-stack_id", false, false);
     PXOPT_LOOKUP_STR(state, config->args, "-state", true, false);
-
-    if (state) {
+    PXOPT_LOOKUP_STR(label, config->args, "-label", false, false);
+
+    // Hack-y work around to make stacktool more like the other tools, without breaking other stuff (hopefully).
+
+    if ((state)&&(stack_id)) {
         // set detRun.state to state
         return setstackRunState(config, stack_id, state);
     }
 
-    return true;
+    if ((state)&&(label)) {
+      return setstackRunStateByLabel(config, label, state);
+    }
+
+    psError(PS_ERR_UNKNOWN, false, "Required options not found.");
+    return false;
 }
 
@@ -1006,4 +1015,24 @@
 }
 
+static bool setstackRunStateByLabel(pxConfig *config, const char *label, const char *state)
+{
+    PS_ASSERT_PTR_NON_NULL(state, false);
+
+    // check that state is a valid string value
+    if (!pxIsValidState(state)) {
+        psError(PS_ERR_UNKNOWN, false, "invalid stackRun state: %s", state);
+        return false;
+    }
+
+    char *query = "UPDATE stackRun SET state = '%s' WHERE label = '%s'";
+    if (!p_psDBRunQueryF(config->dbh, query, state, label)) {
+        psError(PS_ERR_UNKNOWN, false,
+                "failed to change state for label %s", label);
+        return false;
+    }
+
+    return true;
+}
+
 static bool pendingcleanuprunMode(pxConfig *config)
 {
Index: trunk/ippTools/src/stacktoolConfig.c
===================================================================
--- trunk/ippTools/src/stacktoolConfig.c	(revision 25793)
+++ trunk/ippTools/src/stacktoolConfig.c	(revision 25800)
@@ -108,5 +108,6 @@
     psMetadataAddS64(updaterunArgs, PS_LIST_TAIL, "-stack_id", 0,            "define stack ID (required)", 0);
     psMetadataAddStr(updaterunArgs, PS_LIST_TAIL, "-state", 0,            "set state (required)", NULL);
-
+    psMetadataAddStr(updaterunArgs, PS_LIST_TAIL, "-label", 0,            "define by label instead of stack ID", 0);
+    
     // -addinputskyfile
     psMetadata *addinputskyfileArgs = psMetadataAlloc();
Index: trunk/ippTools/src/warptool.c
===================================================================
--- trunk/ippTools/src/warptool.c	(revision 25793)
+++ trunk/ippTools/src/warptool.c	(revision 25800)
@@ -1709,12 +1709,30 @@
     PXOPT_LOOKUP_STR(skycell_id, config->args, "-skycell_id", true, false);
     PXOPT_LOOKUP_S16(fault, config->args, "-fault", false, false);
-
-    psString query = pxDataGet("warptool_updateskyfile.sql");
-
-    if (!p_psDBRunQueryF(config->dbh, query, fault, warp_id, skycell_id)) {
-        psError(PS_ERR_UNKNOWN, false, "database error");
-        return false;
-    }
-    psFree(query);
+    PXOPT_LOOKUP_STR(state, config->args, "-set_state", false, false);
+
+    if (!state) {
+      psString query = pxDataGet("warptool_updateskyfile.sql");
+      
+      if (!p_psDBRunQueryF(config->dbh, query, fault, warp_id, skycell_id)) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        return false;
+      }
+      psFree(query);
+    }
+    else {
+      if (strcmp(state,"error_cleaned") == 0) {
+	change_skyfile_data_state(config,"error_cleaned","goto_cleaned");
+      }
+      else if (strcmp(state, "error_scrubbed") == 0) {
+	change_skyfile_data_state(config,"error_scrubbed","goto_scrubbed");
+      }
+      else if (strcmp(state, "error_purged") == 0) {
+	change_skyfile_data_state(config,"error_purged","goto_purged");
+      }
+      else {
+	psError(PS_ERR_UNKNOWN, false, "unhandled state given");
+	return(false);
+      }
+    }
 
     return true;
Index: trunk/ippTools/src/warptoolConfig.c
===================================================================
--- trunk/ippTools/src/warptoolConfig.c	(revision 25793)
+++ trunk/ippTools/src/warptoolConfig.c	(revision 25800)
@@ -305,5 +305,6 @@
     psMetadataAddStr(updateskyfileArgs, PS_LIST_TAIL, "-skycell_id", 0, "skycell ID to update", NULL);
     psMetadataAddS16(updateskyfileArgs, PS_LIST_TAIL, "-fault",  0,      "new fault code", 0);
-
+    psMetadataAddStr(updateskyfileArgs, PS_LIST_TAIL, "-set_state", 0,   "set state", 0);
+    
     // -exportrun
     psMetadata *exportrunArgs = psMetadataAlloc();