diff --git a/lib/Doctrine/deploy/AddCertificationStatuses.php b/lib/Doctrine/deploy/AddCertificationStatuses.php
index a95afedc9..f931b79ac 100644
--- a/lib/Doctrine/deploy/AddCertificationStatuses.php
+++ b/lib/Doctrine/deploy/AddCertificationStatuses.php
@@ -2,9 +2,9 @@
 
 require_once __DIR__ . "/../bootstrap.php";
 require_once __DIR__ . "/AddUtils.php";
-/* AddNGIs.php: Loads a list of cert statuses from an XML file and
- * inserts them into the doctrine prototype.
- * XML format is the xml input format of the cert status seed data
+/* AddCertificationStatuses.php: Loads a list of cert statuses from
+ * an XML file and inserts them into the doctrine prototype.
+ * XML format is the xml input format of the cert status seed data.
  */
 $certStatsFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
     "/CertificationStatuses.xml";
diff --git a/lib/Doctrine/deploy/AddDowntimes.php b/lib/Doctrine/deploy/AddDowntimes.php
index da43206fc..4e9f5c088 100644
--- a/lib/Doctrine/deploy/AddDowntimes.php
+++ b/lib/Doctrine/deploy/AddDowntimes.php
@@ -30,10 +30,9 @@
 // Hack: the above SEs appear twice with the same service type. (nightmare)
 // However in most cases both SEs share the same downtimes...
 
-// AddDowntimes.php: Loads a list of downtimes  from an
+// AddDowntimes.php: Loads a list of downtimes from an
 // XML file and inserts them into the doctrine prototype.
-// XML format is the output from get_service_endpoints PI query.
-//
+// XML format is the output from get_downtime PI query.
 
 
 $allDowntimes = array();
@@ -57,14 +56,17 @@
     $downtime = null;
     // See if we've already entered a downtime with this prom ID
     if (isset($allDowntimes[$promId])) {
-        // load $downtime from db by $promId rather than loading from global
+        // Load $downtime from db by $promId rather than loading from global
         // array. This assumes xml ID attribute (without 'G0' appended) is
         // the same as xml PRIMARY_KEY attribute.
         //
         // $downtime = $entityManager->createQuery("select d FROM Downtime " .
         //     "d WHERE d.primaryKey = ?1")
-        //   ->setParameter(1, (string) $promId.'G0')
-        //   ->getResult();
+        //                           ->setParameter(
+        //                               1,
+        //                               (string) $promId.'G0'
+        //                           )
+        //                           ->getResult();
         $downtime = $allDowntimes[$promId];
     }
 
@@ -78,7 +80,7 @@
         );
 
         // There are some edge cases where findSEs returns
-        // more than one SE (see the comment at the top of this file)
+        // more than one SE (see the comment at the top of this file).
         // However if the downtime isn't yet created we always
         // link to the first SE found.
         if (!isset($services[0])) {
@@ -141,7 +143,7 @@
                 // Check whether this exception is caused by a known issue
                 // with duplicate SEs (see comment at the top of the file).
                 // Issue is known if two SEs are found and the hostname is
-                // a known duplicate
+                // a known duplicate.
                 $twoSes = false;
                 if (count($services) == 2) {
                     $twoSes = true;
diff --git a/lib/Doctrine/deploy/AddInfrastructures.php b/lib/Doctrine/deploy/AddInfrastructures.php
index c2814b76c..f28e7dd6a 100644
--- a/lib/Doctrine/deploy/AddInfrastructures.php
+++ b/lib/Doctrine/deploy/AddInfrastructures.php
@@ -3,7 +3,7 @@
 require_once __DIR__ . "/../bootstrap.php";
 require_once __DIR__ . "/AddUtils.php";
 
-/* AddNGIs.php: Loads a list of infrastructures from an XML file and
+/* AddInfrastructures.php: Loads a list of infrastructures from an XML file and
  * inserts them into the doctrine prototype.
  * XML format is the xml input production status format.
  */
diff --git a/lib/Doctrine/deploy/AddNGIRoles.php b/lib/Doctrine/deploy/AddNGIRoles.php
index 7894f63a4..d21f103f8 100644
--- a/lib/Doctrine/deploy/AddNGIRoles.php
+++ b/lib/Doctrine/deploy/AddNGIRoles.php
@@ -19,7 +19,7 @@
             continue;
         }
 
-        // get roletype entity
+        // Get roletype entity
         $dql = "SELECT rt FROM RoleType rt WHERE rt.name = :roleType";
         $roleTypes = $entityManager->createQuery($dql)
                                    ->setParameter(
@@ -27,8 +27,9 @@
                                        (string) $role->USER_ROLE
                                    )
                                    ->getResult();
+
         // /* Error checking: ensure each role type refers to exactly
-         // * one role type*/
+         // * one role type */
         if (count($roleTypes) !== 1) {
             throw new Exception(count($roleTypes) . " role types found " .
                 "with name: " . $role->USER_ROLE);
@@ -59,8 +60,8 @@
             $doctrineUser = $doctrineUser;
         }
 
-        // Check for invalid NGIs and skip
-        // typically these are decomissioned ROCs
+        // Check for invalid NGIs and skip.
+        // Typically these are decomissioned ROCs.
         if (
             $role->ON_ENTITY == 'GridIreland'
             || $role->ON_ENTITY == 'NGS'
@@ -71,7 +72,7 @@
             continue;
         }
 
-        // get ngi entity
+        // Get ngi entity
         $ngiName = (string) $role->ON_ENTITY;
         $dql = "SELECT n FROM NGI n WHERE n.name = :ngi";
         $ngis = $entityManager->createQuery($dql)
@@ -80,6 +81,7 @@
                                   $ngiName
                               )
                               ->getResult();
+
         // /* Error checking: ensure each "ngi" refers to exactly
          // * one ngi */
         if (count($ngis) !== 1) {
@@ -91,7 +93,8 @@
             $ngi = $ngi;
         }
 
-        //check that the role is not a duplicate (v4 data contaisn duplicates)
+        // Check that the role is not a duplicate
+        // (v4 data contains duplicates)
         $ExistingUserRoles = $doctrineUser->getRoles();
         $thisIsADuplicateRole=false;
         foreach ($ExistingUserRoles as $role) {
diff --git a/lib/Doctrine/deploy/AddNGIs.php b/lib/Doctrine/deploy/AddNGIs.php
index 58441c329..30f02a7cc 100644
--- a/lib/Doctrine/deploy/AddNGIs.php
+++ b/lib/Doctrine/deploy/AddNGIs.php
@@ -16,11 +16,12 @@
 $egiProject = $entityManager->getRepository('Project')
                             ->findOneBy(array("name" => "EGI"));
 
-//Find the EGI scope tag
+// Find the EGI scope tag
 $egiScope = $entityManager->getRepository('Scope')
                           ->findOneBy(array("name" => "EGI"));
 
-//Add Local Scope so specified NGI is not part of EGI project
+// Add Local Scope so that the specified NGI is
+// not part of the EGI project
 $localScope = $entityManager->getRepository('Scope')
                             ->findOneBy(array("name" => "Local"));
 
@@ -68,7 +69,7 @@
             // '12-JAN-10 14.12.56.000000'
             $cdateonString = (string) $value;
 
-            //convert to date time
+            // Convert to date time
             $creationDate = DateTime::createFromFormat(
                 'd-M-y G.i.s.u',
                 $cdateonString,
@@ -94,12 +95,12 @@
     //if ($cdateon == null) throw new Exception("CDATEON is null");
     //$doctrineNgi->setCreationDate($cdateon);
 
-    // if the NGI has id 67518 (NGI_HU) do not add it to EGI Project
+    // If the NGI has id 67518 (NGI_HU) do not add it to EGI Project
     if ($objectID == "67518") {
         $doctrineNgi->addScope($localScope);
         $entityManager->persist($doctrineNgi);
     } else {
-        // add NGI to EGI project and give it EGI scope
+        // Add NGI to EGI project and give it EGI scope
         $egiProject->addNgi($doctrineNgi);
         $doctrineNgi->addScope($egiScope);
         $entityManager->persist($doctrineNgi);
@@ -107,6 +108,6 @@
 
 }
 
-// don't need to merge egiProject
-//$entityManager->merge($egiProject);
+// Don't need to merge egiProject
+// $entityManager->merge($egiProject);
 $entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddProjectRoles.php b/lib/Doctrine/deploy/AddProjectRoles.php
index f626ea76e..140d76bb3 100644
--- a/lib/Doctrine/deploy/AddProjectRoles.php
+++ b/lib/Doctrine/deploy/AddProjectRoles.php
@@ -4,7 +4,7 @@
 require_once __DIR__ . "/AddUtils.php";
 
 /**
- * AddEgiRoles.php: Loads a list of roles from the get_user PI
+ * AddProjectRoles.php: Loads a list of roles from the get_user PI
  * query output (XML), finds what project entity the role is over,
  * if the project entity refers to exactly one project the role is
  * added to that project and inserted into the doctrine prototype.
@@ -28,7 +28,7 @@
             continue;
         }
 
-        // get roletype entity
+        // Get roletype entity
         $dql = "SELECT rt FROM RoleType rt WHERE rt.name = :roleType";
         $roleTypes = $entityManager->createQuery($dql)
                                    ->setParameter(
@@ -36,8 +36,9 @@
                                        (string) $role->USER_ROLE
                                    )
                                    ->getResult();
+
         // /* Error checking: ensure each role type refers to exactly
-         // * one role type*/
+         // * one role type */
         if (count($roleTypes) !== 1) {
             throw new Exception(count($roleTypes) . " role types found " .
                 "with name: " . $role->USER_ROLE);
diff --git a/lib/Doctrine/deploy/AddScopes.php b/lib/Doctrine/deploy/AddScopes.php
index 2d52e1d1f..9b20f53a4 100644
--- a/lib/Doctrine/deploy/AddScopes.php
+++ b/lib/Doctrine/deploy/AddScopes.php
@@ -3,7 +3,7 @@
 require_once __DIR__ . "/../bootstrap.php";
 require_once __DIR__ . "/AddUtils.php";
 
-/* AddNGIs.php: Loads a list of scopes from an XML file and
+/* AddScopes.php: Loads a list of scopes from an XML file and
  * inserts them into the doctrine prototype.
  * XML format is the xml input format for scope data
  */
diff --git a/lib/Doctrine/deploy/AddServiceEndpoints.php b/lib/Doctrine/deploy/AddServiceEndpoints.php
index c2c44f2bc..d7827e489 100644
--- a/lib/Doctrine/deploy/AddServiceEndpoints.php
+++ b/lib/Doctrine/deploy/AddServiceEndpoints.php
@@ -41,7 +41,7 @@
 
 foreach ($ses as $xmlSe) {
     $doctrineSe = new Service();
-    // get the hosting site entity
+    // Get the hosting site entity
     $dql = "SELECT s from Site s WHERE s.shortName = ?1";
     $parentSites = $entityManager->createQuery($dql)
                                  ->setParameter(
@@ -64,7 +64,7 @@
 
     $doctrineSe->setParentSiteDoJoin($parentSite);
 
-    // get the hosting service type
+    // Get the hosting service type
     $dql = "SELECT s from ServiceType s WHERE s.name = ?1";
     $sts = $entityManager->createQuery($dql)
                          ->setParameter(
@@ -117,7 +117,7 @@
             " for SE " . $xmlSe->HOSTNAME);
     }
 
-    //set creation date
+    // Set creation date
     $creationDate = new \DateTime("now", new DateTimeZone('UTC'));
 
 
diff --git a/lib/Doctrine/deploy/AddServiceGroupRoles.php b/lib/Doctrine/deploy/AddServiceGroupRoles.php
index 81f0f1a5c..38a556f33 100644
--- a/lib/Doctrine/deploy/AddServiceGroupRoles.php
+++ b/lib/Doctrine/deploy/AddServiceGroupRoles.php
@@ -19,7 +19,7 @@
             continue;
         }
 
-        // get roletype entity
+        // Get roletype entity
         $userRole = (string) $role->USER_ROLE;
         $dql = "SELECT rt FROM RoleType rt WHERE rt.name = :roleType";
         $roleTypes = $entityManager->createQuery($dql)
@@ -65,7 +65,7 @@
         // Set $doctrineUser as the first and only user in the users array
         $doctrineUser = $users[0];
 
-        // get serviceGroup entity
+        // Get serviceGroup entity
         $sgName = (string) $role->ON_ENTITY;
         $dql = "SELECT sg FROM ServiceGroup sg WHERE " .
             "sg.name = :service_group";
diff --git a/lib/Doctrine/deploy/AddSiteRoles.php b/lib/Doctrine/deploy/AddSiteRoles.php
index b3a1e6315..68fe495d2 100644
--- a/lib/Doctrine/deploy/AddSiteRoles.php
+++ b/lib/Doctrine/deploy/AddSiteRoles.php
@@ -4,7 +4,7 @@
 require_once __DIR__ . "/AddUtils.php";
 
 /**
- * AddNGIs.php: Loads a list of Site roles from an XML file and
+ * AddSiteRoles.php: Loads a list of Site roles from an XML file and
  * inserts them into the doctrine prototype.
  * XML format is the output from get_user_doctrine PI query.
  */
@@ -24,8 +24,7 @@
             continue;
         }
 
-        // Find the role type
-        // get the roletype entity
+        // Find the role type and get the roletype entity
         $dql = "SELECT rt FROM RoleType rt WHERE rt.name = ?1";
         $roleTypes = $entityManager->createQuery($dql)
                                    ->setParameter(
@@ -33,6 +32,7 @@
                                        (string) $role->USER_ROLE
                                    )
                                    ->getResult();
+
         // /* Error checking: ensure each role type refers to exactly
         //  * one role type */
         if (count($roleTypes) !== 1) {
@@ -73,14 +73,14 @@
             throw new Exception("Not a doctrine user");
         }
 
-        // Check for invalid sites and skip adding this role
-        // typically these sites don't have an NGI,
-        // country or production status
+        // Check for invalid sites and skip adding this role.
+        // Typically these sites don't have an NGI,
+        // country or production status.
         if (isBad((string) $role->ON_ENTITY)) {
             continue;
         }
 
-        // get the site entity
+        // Get the site entity
         $dql = "SELECT s FROM Site s WHERE s.shortName = ?1";
         $sites = $entityManager->createQuery($dql)
                                ->setParameter(
@@ -88,6 +88,7 @@
                                    (string) $role->ON_ENTITY
                                )
                                ->getResult();
+
         // /* Error checking: ensure each "site" refers to exactly
          // * one site */
         if (count($sites) !== 1) {
@@ -103,7 +104,8 @@
             throw new Exception("Not a doctrine site");
         }
 
-        //check that the role is not a duplicate (v4 data contaisn duplicates)
+        // Check that the role is not a duplicate
+        // (v4 data contains duplicates)
         $ExistingUserRoles = $doctrineUser->getRoles();
         $thisIsADuplicateRole=false;
         foreach ($ExistingUserRoles as $role) {
diff --git a/lib/Doctrine/deploy/AddSites.php b/lib/Doctrine/deploy/AddSites.php
index 3f6296e5c..601e6f850 100644
--- a/lib/Doctrine/deploy/AddSites.php
+++ b/lib/Doctrine/deploy/AddSites.php
@@ -20,7 +20,7 @@
     // Check whether this site has a larger v4 primary key
     // than any other recorded so far
     $v4pkGO = trim((string) $xmlSite->PRIMARY_KEY);
-    // isolate just the number part (slice the 'GO' off the end)
+    // Isolate just the number part (slice the 'GO' off the end)
     $v4pk = (int) substr($v4pkGO, 0, strlen($v4pkGO)-2);
     if ($v4pk > $largestV4SitePk) {
         $largestV4SitePk = $v4pk;
@@ -53,7 +53,7 @@
     $doctrineSite->setAlarmEmail((string) $xmlSite->ALARM_EMAIL);
     $doctrineSite->setHelpdeskEmail((string) $xmlSite->HELPDESKEMAIL);
 
-    // get the parent NGI entity
+    // Get the parent NGI entity
     $dql = "SELECT n FROM NGI n WHERE n.name = ?1";
     $parentNgis = $entityManager->createQuery($dql)
                                 ->setParameter(
@@ -75,7 +75,7 @@
 
     $doctrineSite->setNgiDoJoin($parentNgi);
 
-    // get the target infrastructure
+    // Get the target infrastructure
     $dql = "SELECT i FROM Infrastructure i WHERE i.name = :name";
     $infs = $entityManager->createQuery($dql)
                           ->setParameter(
@@ -97,7 +97,7 @@
 
     $doctrineSite->setInfrastructure($inf);
 
-    // get the cert status
+    // Get the cert status
     $dql = "SELECT c FROM CertificationStatus c WHERE c.name = ?1";
     $certStatuses = $entityManager->createQuery($dql)
                                   ->setParameter(
@@ -126,7 +126,7 @@
         )
     );
 
-    // get / set the country
+    // Get / set the country
     $dql = "SELECT c FROM Country c WHERE c.name = ?1";
     $countries = $entityManager->createQuery($dql)
                                ->setParameter(
@@ -149,7 +149,7 @@
     $doctrineSite->setCountry($country);
 
 
-    // get the Tier (optional value)
+    // Get the Tier (optional value)
     $dql = "SELECT t FROM Tier t WHERE t.name = ?1";
     $tiers = $entityManager->createQuery($dql)
                            ->setParameter(
@@ -168,7 +168,7 @@
         $doctrineSite->setTier($tier);
     }
 
-    // get the SubGrid (optional value)
+    // Get the SubGrid (optional value)
     $dql = "SELECT s FROM SubGrid s WHERE s.name = ?1";
     $subGrids = $entityManager->createQuery($dql)
                               ->setParameter(
@@ -189,7 +189,7 @@
 
 
 
-    //set creation date
+    // Set creation date
     $creationDate = new \DateTime(
         "now",
         new DateTimeZone('UTC')
@@ -203,7 +203,7 @@
     // store this date as an attribute on the Site.
     foreach ($xmlCertStatusLinkDates as $xmlCertStatusLinkDate) {
         $targetSiteName = (string) $xmlCertStatusLinkDate->name;
-        // only interested in the current site
+        // Only interested in the current site
         if ($targetSiteName == $doctrineSite->getShortName()) {
             // '01-JUL-13 11.09.10.000000 AM' which has the php datetime
             // format of 'd-M-y H.i.s A' provided we
@@ -245,7 +245,7 @@
     // a link/linkType object using the dateOn property.
     foreach ($xmlCertStatusChanges as $xmlCertStatusChange) {
         $targetSiteName = (string) $xmlCertStatusChange->SITE;
-        // only interested in the current site
+        // Only interested in the current site
         if ($targetSiteName == $doctrineSite->getShortName()) {
             $doctrineCertStatusChangeLog = new \CertificationStatusLog();
             $doctrineCertStatusChangeLog->setAddedBy((string)
diff --git a/lib/Doctrine/deploy/AddUsers.php b/lib/Doctrine/deploy/AddUsers.php
index e75ca6124..e7227c535 100644
--- a/lib/Doctrine/deploy/AddUsers.php
+++ b/lib/Doctrine/deploy/AddUsers.php
@@ -43,7 +43,8 @@
             $user->WORKING_HOURS_END);
         $doctrineUser->setAdmin(false);
 
-        // Roughly half of users don't have a home site set
+        // Check if users don't have a homesite set, or
+        // if the homesite is 'bad'.
         if ($user->HOMESITE !== "" && !isBad($user->HOMESITE)) {
             // Get the home site entity
             $dql = "SELECT s from Site s WHERE s.shortName = ?1";
@@ -55,7 +56,7 @@
                             ->getResult();
 
             /* Error checking: ensure each "home site" refers to exactly
-            * one home site */
+             * one home site */
             if (count($homeSites) !== 1) {
                 throw new \Exception(count($homeSites) . " sites found " .
                     "with short name: " . $user->HOMESITE .
diff --git a/lib/Doctrine/deploy/AddUtils.php b/lib/Doctrine/deploy/AddUtils.php
index 9ff328e64..6ec5c60c7 100644
--- a/lib/Doctrine/deploy/AddUtils.php
+++ b/lib/Doctrine/deploy/AddUtils.php
@@ -44,7 +44,7 @@ function isBad($site) {
             'UIS-BUCARAMANGA', 'UTP-PANAMA', 'ITWM-PPS' , 'HU-BERLIN',
             'SCAI-PPS', 'FZK-SC', 'FZK-Test', 'FZK-Test',
             'GRIDOPS-GRIDVIEW', 'GSI-LCG2-PPS',
-            // next lot is from NGI_IE which was deleted.
+            // Next lot is from NGI_IE which was deleted.
             'csTCDie', 'mpUCDie', 'giNUIMie', 'cpDIASie', 'csQUBuk',
             'csUCCie', 'scgNUIGie', 'giITTAie', 'obsARMuk', 'giHECie',
             'giRCSIie', 'giDCUie');
@@ -63,14 +63,14 @@ function isBad($site) {
  * @return \Scope
  */
 function getScope($entityManager, $scope) {
-    // get the scope
+    // Get the scope
     $dql = "SELECT s FROM Scope s WHERE s.name = ?1";
     $scopes = $entityManager->createQuery($dql)
                             ->setParameter(1, $scope)
                             ->getResult();
 
     /* Error checking: ensure each Site's "SCOPE" refers to exactly
-    * one SCOPE */
+     * one SCOPE */
     if (count($scopes) !== 1) {
         throw new Exception(count($scopes) . " SCOPEs found " .
             "with name: " . $scope);