diff --git a/.hgignore b/.hgignore
index 1ab15e04001fa5c8f231c373640cc2f1842eb339..79942641fad50cbc7a37290c173f48b8405f6e83 100644
--- a/.hgignore
+++ b/.hgignore
@@ -6,7 +6,8 @@ cache
 .coverage
 local_env.sh
 coverage_html_report
-lwr_staging
+files/staging
+files/persisted_data
 server.ini
 job_managers.ini
 *.pem
diff --git a/docs/source/files/job_conf_sample_mq.xml b/docs/source/files/job_conf_sample_mq.xml
index 80607c4160cc98319234da441d4152dfbcd596a5..cac3dbff964209d82c446738e6ba37602366239d 100644
--- a/docs/source/files/job_conf_sample_mq.xml
+++ b/docs/source/files/job_conf_sample_mq.xml
@@ -21,7 +21,7 @@
             <!-- Tell Galaxy where files are being store on remote system, no
                  web server it can simply ask for this information.
             -->
-            <param id="jobs_directory">/path/to/remote/lwr/lwr_staging/</param>
+            <param id="jobs_directory">/path/to/remote/pulsar/files/staging/</param>
             <!-- Invert file transfers - have LWR initiate downloads during preprocessing
                  and uploads during postprocessing. -->
             <param id="default_file_action">remote_transfer</param>
diff --git a/docs/source/upgrading.rst b/docs/source/upgrading.rst
index 5235e1de6b4a61a1442388bd81b7847ab1a422b2..d81b0b9878ef000f0cd06fba1c216065003c84c8 100644
--- a/docs/source/upgrading.rst
+++ b/docs/source/upgrading.rst
@@ -10,3 +10,4 @@ Rough plan:
 - Rebuild dependencies (and/or virtualenv) if needed.
 - Copy the LWR's server.ini to Pulsar's root directory.
 - Update ``app_factory`` property: ``paste.app_factory = pulsar.web.wsgi:app_factory``
+- If you were using the default values for ``persistence_directory`` and ``staging_directory`` you may wish to update those to the new defaults as well.
diff --git a/persisted_data/info.txt b/files/persisted_data/info.txt
similarity index 100%
rename from persisted_data/info.txt
rename to files/persisted_data/info.txt
diff --git a/pulsar/core.py b/pulsar/core.py
index df1f53bba6b265225fa59358563de29465406f60..c07fcf7185c6b9063be6f33fdc646a1a9fc7eb69 100644
--- a/pulsar/core.py
+++ b/pulsar/core.py
@@ -17,8 +17,9 @@ from logging import getLogger
 log = getLogger(__name__)
 
 DEFAULT_PRIVATE_KEY = None
-DEFAULT_STAGING_DIRECTORY = "lwr_staging"
-DEFAULT_PERSISTENCE_DIRECTORY = "persisted_data"
+DEFAULT_FILES_DIRECTORY = "files"
+DEFAULT_STAGING_DIRECTORY = os.path.join(DEFAULT_FILES_DIRECTORY, "staging")
+DEFAULT_PERSISTENCE_DIRECTORY = os.path.join(DEFAULT_FILES_DIRECTORY, "persisted_data")
 
 
 NOT_WHITELIST_WARNING = "Starting the LWR without a toolbox to white-list." + \
diff --git a/server.ini.sample b/server.ini.sample
index 6592dd76a26f18805757a28e4267d7d04fbb24e4..a246dae0d3f85725bc377a91e3bfbe479ce44cf0 100644
--- a/server.ini.sample
+++ b/server.ini.sample
@@ -20,8 +20,8 @@ host = localhost
 paste.app_factory = pulsar.web.wsgi:app_factory
 
 ## Directory to stage files to. This should likely be updated to point
-## to an absolute path, such as /tmp/lwr_staging or C:\\lwr_staging
-staging_directory = lwr_staging
+## to an absolute path, such as /tmp/pulsar_staging or C:\\pulsar_staging
+staging_directory = files/staging
 
 ## Private key or password that must be sent as part of the request to
 ## authorize use. If security is important, please use this in
@@ -35,7 +35,7 @@ staging_directory = lwr_staging
 ## do this). If user the LWR runs as cannot write to the LWR root
 ## directory, this should be updated to point to some directory which
 ## it can write to.
-persistence_directory = persisted_data
+persistence_directory = files/persisted_data
 
 ## How are ids assigned. galaxy (default) just passes through ids as
 ## is. Setting this uuid assigns each job a UUID, this is strongly