diff --git a/data_manager_conf.xml.sample b/config/data_manager_conf.xml.sample
similarity index 100%
rename from data_manager_conf.xml.sample
rename to config/data_manager_conf.xml.sample
diff --git a/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
similarity index 100%
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rename to config/datatypes_conf.xml.sample
diff --git a/demo_sequencer_wsgi.ini.sample b/config/demo_sequencer_wsgi.ini.sample
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diff --git a/external_service_types_conf.xml.sample b/config/external_service_types_conf.xml.sample
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diff --git a/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced
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diff --git a/job_conf.xml.sample_basic b/config/job_conf.xml.sample_basic
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diff --git a/job_metrics_conf.xml.sample b/config/job_metrics_conf.xml.sample
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diff --git a/job_resource_params_conf.xml.sample b/config/job_resource_params_conf.xml.sample
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diff --git a/migrated_tools_conf.xml.sample b/config/migrated_tools_conf.xml.sample
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diff --git a/object_store_conf.xml.sample b/config/object_store_conf.xml.sample
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diff --git a/openid_conf.xml.sample b/config/openid_conf.xml.sample
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diff --git a/reports_wsgi.ini.sample b/config/reports_wsgi.ini.sample
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diff --git a/shed_data_manager_conf.xml.sample b/config/shed_data_manager_conf.xml.sample
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diff --git a/shed_tool_conf.xml.sample b/config/shed_tool_conf.xml.sample
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diff --git a/shed_tool_data_table_conf.xml.sample b/config/shed_tool_data_table_conf.xml.sample
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diff --git a/tool_conf.xml.main b/config/tool_conf.xml.main
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diff --git a/tool_conf.xml.sample b/config/tool_conf.xml.sample
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diff --git a/tool_data_table_conf.xml.sample b/config/tool_data_table_conf.xml.sample
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diff --git a/tool_shed_wsgi.ini.sample b/config/tool_shed_wsgi.ini.sample
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diff --git a/tool_sheds_conf.xml.sample b/config/tool_sheds_conf.xml.sample
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diff --git a/universe_wsgi.ini.sample b/config/universe_wsgi.ini.sample
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diff --git a/distributed_object_store_conf.xml.sample b/distributed_object_store_conf.xml.sample
deleted file mode 100644
index 30cbaacc62f..00000000000
--- a/distributed_object_store_conf.xml.sample
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0"?>
-<backends>
-    <backend id="files1" type="disk" weight="1">
-        <files_dir path="database/files1"/>
-        <extra_dir type="temp" path="database/tmp1"/>
-        <extra_dir type="job_work" path="database/job_working_directory1"/>
-    </backend>
-    <backend id="files2" type="disk" weight="1">
-        <files_dir path="database/files2"/>
-        <extra_dir type="temp" path="database/tmp2"/>
-        <extra_dir type="job_work" path="database/job_working_directory2"/>
-    </backend>
-</backends>
diff --git a/tool_data_table_conf.xml.oldlocstyle b/tool_data_table_conf.xml.oldlocstyle
deleted file mode 100644
index e6fbfa81d7f..00000000000
--- a/tool_data_table_conf.xml.oldlocstyle
+++ /dev/null
@@ -1,73 +0,0 @@
-<!-- Use this file if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
-    </table>
-    <!-- Locations of indexes in the BFAST mapper format -->
-    <table name="bfast_indexes" comment_char="#">
-        <columns>value, dbkey, formats, name, path</columns>
-        <file path="tool-data/bfast_indexes.loc" />
-    </table>
-    <!-- Locations of nucleotide (mega)blast databases -->
-    <table name="blastdb" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/blastdb.loc" />
-    </table>
-    <!-- Locations of protein (mega)blast databases -->
-    <table name="blastdb_p" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/blastdb_p.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie mapper format -->
-    <table name="bowtie_indexes" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/bowtie_indices.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie color mapper format -->
-    <table name="bowtie_indexes_color" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/bowtie_indices_color.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA mapper format -->
-    <table name="bwa_indexes" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/bwa_index.loc" />
-    </table>
-    <!-- Locations of MAF files that have been indexed with bx-python -->
-    <table name="indexed_maf_files">
-        <columns>name, value, dbkey, species</columns>
-        <file path="tool-data/maf_index.loc" />
-    </table>
-    <!-- Locations of fasta files appropriate for NGS simulation -->
-    <table name="ngs_sim_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/ngs_sim_fasta.loc" />
-    </table>
-    <!-- Locations of 2bit sequence files for use in Lastz -->
-    <table name="lastz_seqs" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/lastz_seqs.loc" />
-    </table>
-    <!-- Locations of PerM base index files -->
-    <table name="perm_base_indexes" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/perm_base_index.loc" />
-    </table>
-    <!-- Locations of PerM color index files -->
-    <table name="perm_color_indexes" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/perm_color_index.loc" />
-    </table>
-    <!-- Location of SRMA dict file and other files -->
-    <table name="srma_indexes" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/srma_index.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
-    <table name="tophat_indexes" comment_char="#">
-        <columns>name, value</columns>
-        <file path="tool-data/bowtie_indices.loc" />
-    </table>
-</tables>