This means your preferences will be considered corrupt whenever you switch from the upstream version to the debian package or vice versa.

As one of the JOSM developers, I find this quite unfortunate. Here is a suggested fix: Instead of replacing the "resource://" URLs in the source code directly [1], change the way these URLs are retrieved: First check the /usr/share/josm directory, then inside the jar. Patch attached (untested).


[1] <http://anonscm.debian.org/gitweb/?p=pkg-osm/josm.git;a=commitdiff;h=2a1def7a69795a9d8670dfb387da49acf33fbe5c>
Index: src/org/openstreetmap/josm/io/MirroredInputStream.java
===================================================================
--- src/org/openstreetmap/josm/io/MirroredInputStream.java	(revision 5778)
+++ src/org/openstreetmap/josm/io/MirroredInputStream.java	(working copy)
@@ -81,13 +81,21 @@
             }
         } catch (java.net.MalformedURLException e) {
             if (name.startsWith("resource://")) {
-                fs = getClass().getResourceAsStream(
-                        name.substring("resource:/".length()));
-                if (fs == null)
-                    throw new IOException(tr("Failed to open input stream for resource ''{0}''", name));
-                return;
+                String path = name.substring("resource://".length());
+                File fileRes = new File("/usr/share/josm/" + path);
+                if (fileRes.exists()) {
+                    file = fileRes;
+                } else {
+                    fs = getClass().getResourceAsStream(
+                            name.substring("resource:/".length()));
+                    if (fs == null)
+                        throw new IOException(tr("Failed to open input stream for resource ''{0}''", name));
+                    return;
+                }
             }
-            file = new File(name);
+            if (file == null) {
+                file = new File(name);
+            }
         }
         if (file == null)
             throw new IOException();
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