diff --git a/modules/block/block.install b/modules/block/block.install
index c45b076bf75f75407e8866c2ecd21975c0ca9941..b2ab477d90932ca2cf104bd09116102329858b13 100644
--- a/modules/block/block.install
+++ b/modules/block/block.install
@@ -190,16 +190,12 @@ function block_install() {
  * Implements hook_update_dependencies().
  */
 function block_update_dependencies() {
-  // Block update 7005 needs to query the list of existing text formats and
-  // therefore must run after filter_update_7000().
+  // block_update_7005() needs to query the {filter_format} table to get a list
+  // of existing text formats, so it must run after filter_update_7000(), which
+  // creates that table.
   $dependencies['block'][7005] = array(
     'filter' => 7000,
   );
-  // Ensure that format columns are only changed after Filter module has changed
-  // the primary records.
-  $dependencies['block'][7007] = array(
-    'filter' => 7010,
-  );
 
   return $dependencies;
 }
diff --git a/modules/comment/comment.install b/modules/comment/comment.install
index 120467fd0594d0d7e3e88e7658655dae6ef987f2..cda3c308d5f485f4225ae5db08c012bffe61eb40 100644
--- a/modules/comment/comment.install
+++ b/modules/comment/comment.install
@@ -83,14 +83,16 @@ function comment_modules_enabled($modules) {
  * Implements hook_update_dependencies().
  */
 function comment_update_dependencies() {
-  // Comment update 7005 creates the comment body field and therefore must run
-  // after text module has been enabled and entities have been updated.
+  // comment_update_7005() creates the comment body field and therefore must
+  // run after all Field modules have been enabled, which happens in
+  // system_update_7027().
   $dependencies['comment'][7005] = array(
-    'system' => 7021,
+    'system' => 7027,
   );
 
-  // Comment update 7006 needs to query the list of existing text formats and
-  // therefore must run after filter_update_7000().
+  // comment_update_7006() needs to query the {filter_format} table to get a
+  // list of existing text formats, so it must run after filter_update_7000(),
+  // which creates that table.
   $dependencies['comment'][7006] = array(
     'filter' => 7000,
   );
diff --git a/modules/field/modules/text/text.install b/modules/field/modules/text/text.install
index b9bd25f19932640b6e9d6bb878af5c78b43fd208..61be748ac4055f30b7fff2aca8fb9ed70ab699a2 100644
--- a/modules/field/modules/text/text.install
+++ b/modules/field/modules/text/text.install
@@ -66,19 +66,6 @@ function text_field_schema($field) {
   );
 }
 
-/**
- * Implements hook_update_dependencies().
- */
-function text_update_dependencies() {
-  // Ensure that format columns are only changed after Filter module has changed
-  // the primary records.
-  $dependencies['text'][7000] = array(
-    'filter' => 7010,
-  );
-
-  return $dependencies;
-}
-
 /**
  * Change text field 'format' columns into varchar.
  */
diff --git a/modules/filter/filter.install b/modules/filter/filter.install
index 84512cd589f404b61d4903e7dc4af8d7e13fd188..19fd8aa18297a18294e2294fae3b139607d07814 100644
--- a/modules/filter/filter.install
+++ b/modules/filter/filter.install
@@ -152,8 +152,9 @@ function filter_install() {
  * Implements hook_update_dependencies().
  */
 function filter_update_dependencies() {
-  // Filter update 7007 migrates permissions and therefore needs to run after
-  // the {role} table is properly set up.
+  // filter_update_7005() migrates role permissions and therefore must run
+  // after the {role} and {role_permission} tables are properly set up, which
+  // happens in user_update_7007().
   $dependencies['filter'][7005] = array(
     'user' => 7007,
   );
diff --git a/modules/node/node.install b/modules/node/node.install
index 2498091fc533896ac2e885235a5d50e6ffc41d8c..d33f095f07cf493cf199d3f1742f8278d3c9f330 100644
--- a/modules/node/node.install
+++ b/modules/node/node.install
@@ -447,17 +447,23 @@ function node_install() {
  * Implements hook_update_dependencies().
  */
 function node_update_dependencies() {
-  // Node update 7006 migrates node data to fields and therefore must run after
-  // the Field module has been enabled, but before upgrading field data.
+  // node_update_7006() migrates node data to fields and therefore must run
+  // after all Field modules have been enabled, which happens in
+  // system_update_7027(). It also needs to query the {filter_format} table to
+  // get a list of existing text formats, so it must run after
+  // filter_update_7000(), which creates that table.
   $dependencies['node'][7006] = array(
-    'system' => 7049,
-    // It must also run after filter_update_7000() because it needs to query
-    // the list of existing text formats.
+    'system' => 7027,
     'filter' => 7000,
   );
-  $dependencies['system'][7050] = array(
-    'node' => 7006,
+
+  // node_update_7008() migrates role permissions and therefore must run after
+  // the {role} and {role_permission} tables are properly set up, which happens
+  // in user_update_7007().
+  $dependencies['node'][7008] = array(
+    'user' => 7007,
   );
+
   return $dependencies;
 }
 
diff --git a/modules/system/system.install b/modules/system/system.install
index e55c7cf3aa7e6d7f8c6fe2e8c0c31dca293a6e46..6cbbb9ed018c543237c6985b94eec687fe902b0d 100644
--- a/modules/system/system.install
+++ b/modules/system/system.install
@@ -1681,11 +1681,19 @@ function system_update_last_removed() {
  * Implements hook_update_dependencies().
  */
 function system_update_dependencies() {
-  // Update 7053 adds new blocks, so make sure the block tables are updated.
+  // system_update_7053() queries the {block} table, so it must run after
+  // block_update_7002(), which creates that table.
   $dependencies['system'][7053] = array(
     'block' => 7002,
   );
 
+  // system_update_7067() migrates role permissions and therefore must run
+  // after the {role} and {role_permission} tables are properly set up, which
+  // happens in user_update_7007().
+  $dependencies['system'][7067] = array(
+    'user' => 7007,
+  );
+
   return $dependencies;
 }
 
@@ -1866,9 +1874,6 @@ function system_update_7005() {
 
 /**
  * Convert to new method of storing permissions.
- *
- * This update is in system.install rather than user.install so that
- * all modules can use the updated permission scheme during their updates.
  */
 function system_update_7007() {
   // Copy the permissions from the old {permission} table to the new {role_permission} table.
diff --git a/modules/taxonomy/taxonomy.install b/modules/taxonomy/taxonomy.install
index 68fbc7804a99922d6b00b432c6c9b7c5b3c48686..f442c95ef175347987efa73bc80e7939b4b35c9d 100644
--- a/modules/taxonomy/taxonomy.install
+++ b/modules/taxonomy/taxonomy.install
@@ -251,26 +251,11 @@ function taxonomy_field_schema($field) {
  * Implements hook_update_dependencies().
  */
 function taxonomy_update_dependencies() {
-  // Taxonomy update 7002 creates comment Field API bundles and therefore must
-  // run after the Field module has been enabled, but before upgrading field
-  // data.
-  $dependencies['taxonomy'][7002] = array(
-    'system' => 7049,
-  );
-  $dependencies['user'][7006] = array(
-    'taxonomy' => 7002,
-  );
-  $dependencies['system'][7050] = array(
-    'taxonomy' => 7002,
-  );
-  // It also must run before nodes are upgraded to use the Field API.
-  $dependencies['node'][7006] = array(
-    'taxonomy' => 7002,
-  );
-  // Ensure that format columns are only changed after Filter module has changed
-  // the primary records.
-  $dependencies['taxonomy'][7009] = array(
-    'filter' => 7010,
+  // taxonomy_update_7004() migrates taxonomy term data to fields and therefore
+  // must run after all Field modules have been enabled, which happens in
+  // system_update_7027().
+  $dependencies['taxonomy'][7004] = array(
+    'system' => 7027,
   );
 
   return $dependencies;
diff --git a/modules/user/user.install b/modules/user/user.install
index 75fca659014f2d494ce51e9a6962b2e56fe05a01..2867b97ed2c0e772a0b4a303b47f760a1fc96400 100644
--- a/modules/user/user.install
+++ b/modules/user/user.install
@@ -340,25 +340,32 @@ function user_install() {
  * Implements hook_update_dependencies().
  */
 function user_update_dependencies() {
-  // Run all the critical user upgrades before everything.
-  $dependencies['system'][7000] = array(
-    'user' => 7008,
-  );
-  // Both user_update_7006() and user_update_7010() need to query the list of
-  // existing text formats and therefore must run after filter_update_7003().
-  // @todo: move user_update_7006 down below in the upgrade process.
+  // user_update_7006() updates data in the {role_permission} table, so it must
+  // run after system_update_7007(), which populates that table.
   $dependencies['user'][7006] = array(
-    'filter' => 7003,
+    'system' => 7007,
+  );
+
+  // user_update_7010() needs to query the {filter_format} table to get a list
+  // of existing text formats, so it must run after filter_update_7000(), which
+  // creates that table.
+  $dependencies['user'][7010] = array(
+    'filter' => 7000,
   );
-  // user_update_7013 relies on system_update_7060.
+
+  // user_update_7012() uses the file API, which relies on the {file_managed}
+  // table, so it must run after system_update_7034(), which creates that
+  // table.
+  $dependencies['user'][7012] = array(
+    'system' => 7034,
+  );
+
+  // user_update_7013() uses the file usage API, which relies on the
+  // {file_usage} table, so it must run after system_update_7059(), which
+  // creates that table.
   $dependencies['user'][7013] = array(
     'system' => 7059,
   );
-  // Ensure that format columns are only changed after Filter module has changed
-  // the primary records.
-  $dependencies['user'][7015] = array(
-    'filter' => 7010,
-  );
 
   return $dependencies;
 }