diff --git a/lib/galaxy/config.py b/lib/galaxy/config/__init__.py
similarity index 100%
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diff --git a/config/auth_conf.xml.sample b/lib/galaxy/config/sample/auth_conf.xml.sample
similarity index 100%
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diff --git a/config/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
similarity index 100%
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diff --git a/config/tool_sheds_conf.xml.sample b/lib/galaxy/config/sample/tool_sheds_conf.xml.sample
similarity index 100%
rename from config/tool_sheds_conf.xml.sample
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diff --git a/scripts/migrate_tools/0002_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0002_tools.xml
similarity index 100%
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diff --git a/scripts/migrate_tools/0003_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0003_tools.xml
similarity index 100%
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diff --git a/scripts/migrate_tools/0004_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0004_tools.xml
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diff --git a/scripts/migrate_tools/0005_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0005_tools.xml
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diff --git a/scripts/migrate_tools/0006_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0006_tools.xml
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diff --git a/scripts/migrate_tools/0007_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0007_tools.xml
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diff --git a/scripts/migrate_tools/0008_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0008_tools.xml
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diff --git a/scripts/migrate_tools/0009_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0009_tools.xml
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diff --git a/scripts/migrate_tools/0010_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0010_tools.xml
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diff --git a/scripts/migrate_tools/0011_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0011_tools.xml
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diff --git a/scripts/migrate_tools/0012_tools.xml b/lib/tool_shed/galaxy_install/migrate/scripts/0012_tools.xml
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rename from scripts/migrate_tools/0012_tools.xml
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diff --git a/scripts/manage_tools.py b/lib/tool_shed/galaxy_install/migrate/scripts/manage_tools.py
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diff --git a/scripts/migrate_tools/migrate_tools.py b/lib/tool_shed/galaxy_install/migrate/scripts/migrate_tools.py
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rename from scripts/migrate_tools/migrate_tools.py
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diff --git a/scripts/migrate_tools/0002_tools.sh b/scripts/migrate_tools/0002_tools.sh
deleted file mode 100644
index 926aba9529d..00000000000
--- a/scripts/migrate_tools/0002_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml $@
diff --git a/scripts/migrate_tools/0003_tools.sh b/scripts/migrate_tools/0003_tools.sh
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index dfc3bde56b3..00000000000
--- a/scripts/migrate_tools/0003_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml $@
diff --git a/scripts/migrate_tools/0004_tools.sh b/scripts/migrate_tools/0004_tools.sh
deleted file mode 100644
index 40b76956fa2..00000000000
--- a/scripts/migrate_tools/0004_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml $@
diff --git a/scripts/migrate_tools/0005_tools.sh b/scripts/migrate_tools/0005_tools.sh
deleted file mode 100644
index c9f1f3c61d6..00000000000
--- a/scripts/migrate_tools/0005_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml $@
diff --git a/scripts/migrate_tools/0006_tools.sh b/scripts/migrate_tools/0006_tools.sh
deleted file mode 100644
index 1f000ebeca6..00000000000
--- a/scripts/migrate_tools/0006_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml $@
diff --git a/scripts/migrate_tools/0007_tools.sh b/scripts/migrate_tools/0007_tools.sh
deleted file mode 100644
index a6cf948593d..00000000000
--- a/scripts/migrate_tools/0007_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml $@
diff --git a/scripts/migrate_tools/0008_tools.sh b/scripts/migrate_tools/0008_tools.sh
deleted file mode 100644
index 50cafd19936..00000000000
--- a/scripts/migrate_tools/0008_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml $@
diff --git a/scripts/migrate_tools/0009_tools.sh b/scripts/migrate_tools/0009_tools.sh
deleted file mode 100644
index 36f162b141c..00000000000
--- a/scripts/migrate_tools/0009_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml $@
diff --git a/scripts/migrate_tools/0010_tools.sh b/scripts/migrate_tools/0010_tools.sh
deleted file mode 100644
index fde17704dd3..00000000000
--- a/scripts/migrate_tools/0010_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml $@
diff --git a/scripts/migrate_tools/0011_tools.sh b/scripts/migrate_tools/0011_tools.sh
deleted file mode 100644
index a31365804fd..00000000000
--- a/scripts/migrate_tools/0011_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml $@
diff --git a/scripts/migrate_tools/0012_tools.sh b/scripts/migrate_tools/0012_tools.sh
deleted file mode 100644
index 97fbe354d04..00000000000
--- a/scripts/migrate_tools/0012_tools.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml $@