diff -r -u irods-4.2.0.orig/lib/core/src/irods_default_paths.cpp irods-4.2.0/lib/core/src/irods_default_paths.cpp
--- irods-4.2.0.orig/lib/core/src/irods_default_paths.cpp	2016-11-15 06:23:55.000000000 +0000
+++ irods-4.2.0/lib/core/src/irods_default_paths.cpp	2016-12-20 18:03:17.156883399 +0000
@@ -18,7 +18,7 @@
         try {
             boost::filesystem::path path{dl_info.dli_fname};
             path = boost::filesystem::canonical(path);
-            path.remove_filename().remove_filename().remove_filename(); // Removes filename and the two directories (usr and lib) between libirods_common.so and base of irods install
+            path.remove_filename().remove_filename(); // Removes filename and the two directories (usr and lib) between libirods_common.so and base of irods install
             return path;
         } catch(const boost::filesystem::filesystem_error& e) {
             THROW(-1, e.what());
@@ -27,8 +27,7 @@
 
     boost::filesystem::path
     get_irods_config_directory() {
-        boost::filesystem::path path{get_irods_root_directory()};
-        path.append("etc").append("irods");
+        boost::filesystem::path path("/etc/irods");
         return path;
     }
 
diff -r -u irods-4.2.0.orig/scripts/irods/paths.py irods-4.2.0/scripts/irods/paths.py
--- irods-4.2.0.orig/scripts/irods/paths.py	2016-11-15 06:23:55.000000000 +0000
+++ irods-4.2.0/scripts/irods/paths.py	2016-12-21 15:17:07.437864606 +0000
@@ -10,7 +10,7 @@
     return os.path.join(root_directory(), 'var', 'lib', 'irods')
 
 def config_directory():
-    return os.path.join(root_directory(), 'etc', 'irods')
+    return os.path.join(os.path.abspath('/'), 'etc', 'irods')
 
 def plugins_directory():
     return os.path.join(root_directory(), 'usr', 'lib', 'irods', 'plugins')
@@ -37,7 +37,7 @@
 
 def version_path():
     return os.path.join(
-        irods_directory(),
+        home_directory(),
         'VERSION.json')
 
 def hosts_config_path():
@@ -64,7 +64,7 @@
 
 def log_directory():
     return os.path.join(
-        irods_directory(),
+        home_directory(),
         'log')
 
 def control_log_path():
@@ -110,8 +110,7 @@
 def server_bin_directory():
     return os.path.join(
         root_directory(),
-        'usr',
-        'sbin')
+        'bin')
 
 def server_executable():
     return os.path.join(
@@ -132,7 +131,7 @@
     return os.path.join(config_directory(), 'service_account.config')
 
 def genosauth_path():
-    return os.path.join(irods_directory(), 'clients', 'bin', 'genOSAuth')
+    return os.path.join(home_directory(), 'clients', 'bin', 'genOSAuth')
 
 def irods_user_and_group_entries():
     try: