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I also found that when using msysgit on windows, it expects the objects/info/alternates file to have unix line endings. So even if the path is correct, it fetches the packs anyway.
Here is a patch against 1.6.0 which fixes the problem on my system:
diff --git a/src/main/java/org/jenkinsci/plugins/gitclient/CliGitAPIImpl.java b/src/main/java/org/jenkinsci/plugins/gitclient/ index cd6b092..2de9f66 100644 --- a/src/main/java/org/jenkinsci/plugins/gitclient/CliGitAPIImpl.java +++ b/src/main/java/org/jenkinsci/plugins/gitclient/CliGitAPIImpl.java @@ -335,7 +335,8 @@ public class CliGitAPIImpl extends LegacyCompatibleGitAPIImpl { try { File alternates = new File(workspace, ".git/objects/info/alternates"); PrintWriter w = new PrintWriter(alternates); - w.println(new File(referencePath, ".git/objects").getAbsolutePath()); + w.print(new File(referencePath, reference.endsWith(".git") ? "/objects" : ".git/objects").getAbso + w.print("\n"); w.close(); } catch (FileNotFoundException e) { listener.error("Failed to setup reference");