Fix JGit resources not being closed in CLI commands

[pditommaso]

Summary

• Make AssetManager implement Closeable interface
• Wrap AssetManager usage in CLI commands with try-finally blocks to ensure close() is called
• Prevents ~90 second shutdown delays caused by JGit shutdown hooks cleaning up unclosed Repository objects

Problem

JGit registers shutdown hooks when Repository objects are created. When these are not closed via close(), the cleanup runs during JVM shutdown, causing significant delays:

00:56:52.598 [Test worker] DEBUG java.lang.Runtime -- Runtime.exit() called with status: 0
java.lang.Throwable: Runtime.exit(0)
        at java.base/java.lang.Shutdown.logRuntimeExit(Shutdown.java:179)
        at java.base/java.lang.Shutdown.exit(Shutdown.java:160)
        at java.base/java.lang.Runtime.exit(Runtime.java:188)
        at java.base/java.lang.System.exit(System.java:1920)
        at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:75)
00:58:26.391 [ForkJoinPool-1-worker-1] DEBUG o.e.jgit.internal.util.ShutdownHook – Cleanup org.eclipse.jgit.util.FS$FileStoreAttributes$$Lambda/0x000000a801f07ad0@544df82e during JVM shutdown

Note the ~94 second gap between Runtime.exit(0) and JGit cleanup.

Changes

• AssetManager.groovy: Added implements Closeable
• CmdRun.groovy: Wrapped manager usage in try-finally
• CmdPull.groovy: Wrapped manager usages in try-finally
• CmdView.groovy: Wrapped manager usage in try-finally
• CmdClone.groovy: Wrapped manager usage in try-finally
• CmdInfo.groovy: Wrapped manager usage in try-finally
• CmdConfig.groovy: Wrapped manager usage in try-finally
• CmdDrop.groovy: Wrapped manager usage in try-finally

Test plan

• Run make test to verify existing tests pass
• Verify JGit shutdown delay is eliminated

[netlify]

✅ Deploy Preview for nextflow-docs-staging canceled.

Name	Link
🔨 Latest commit	ccbfcb2
🔍 Latest deploy log	https://app.netlify.com/projects/nextflow-docs-staging/deploys/6981bc857fe9530007a40c82