bug: openshell sandbox upload <local-dir> <remote-dir> flattens contents instead of creating named subdirectory

[mjamiv]

Agent Diagnostic

• Loaded openshell-cli skill and walked the sandbox upload command path in crates/openshell-cli/.
• When <local> is a directory, the CLI walks the directory and uploads each entry into <remote> directly. The local directory's name is dropped from the destination path.
• Confirmed by the minimal repro below. Behavior diverges from the standard scp -r and cp -r semantics operators expect from any *nix-style file-transfer tool.
• Agent identified the workaround: tar -czf foo.tgz -C parent foo && openshell sandbox upload <name> foo.tgz /tmp/ && ssh ... 'tar -xzf /tmp/foo.tgz -C <remote>/'. The tarball preserves the source-directory prefix deterministically.

Description

openshell sandbox upload <local-dir> <remote-dir> flattens the local directory's contents into the remote destination instead of creating a subdirectory named after the local directory.

In our case this caused a real near-miss: a directory of content was uploaded into a sibling location alongside existing files at the destination. No data was lost (all uploaded files were new and didn't collide), but the recovery path required a full diff against backups to confirm. A future variant of the same operation could silently shadow files at the destination with no warning.

Reproduction Steps

1. Create a local directory with content:

   mkdir -p /tmp/upload-test/sub
   echo a > /tmp/upload-test/a.txt
   echo b > /tmp/upload-test/sub/b.txt
   

2. Upload it: openshell sandbox upload <name> /tmp/upload-test /sandbox/dest/
3. SSH in and inspect: ssh <sandbox> 'ls /sandbox/dest/'
4. Observed: a.txt sub/ — the upload-test/ prefix is gone; contents are flat in /sandbox/dest/.
5. Expected: upload-test/ containing a.txt and sub/b.txt, mirroring scp -r ./upload-test <remote>:/sandbox/dest/.

Environment

• OpenShell: v0.0.31 host CLI, v0.0.31 supervisor
• OS: Ubuntu 24.04 LTS
• Docker: 27.x
• Cluster image: ghcr.io/nvidia/openshell/cluster:0.0.16

Proposed direction

Two options:

1. Match scp -r / cp -r semantics — preserve the source directory's basename as a subdirectory of the destination. Principle-of-least-surprise fix; aligns with every comparable file-transfer tool.
2. Keep current flatten behavior, add a --preserve-dir flag for the standard semantics, plus a CLI help update calling out the divergence loudly.

I prefer (1). The current behavior is a quiet footgun for any operator with prior file-transfer experience. Cost is one breaking-change note in the release. Happy to convert this to a PR if a maintainer signals direction.

Agent-First Checklist

• I pointed my agent at the repo and had it investigate this issue
• I loaded relevant skills (openshell-cli)
• My agent could not resolve this — the diagnostic above explains the root cause; resolution needs an upstream code change.

[github-actions]

This issue appears to have been opened without an agent investigation.

OpenShell is an agent-first project - please point your coding agent at the repo and have it diagnose this before we triage. Your agent can load skills like debug-openshell-cluster, debug-inference, openshell-cli, and generate-sandbox-policy.

See CONTRIBUTING.md for the full workflow.

[mjamiv]

Both proposed-direction variants are pushed to the fork as reference branches, ready to convert to PRs once a maintainer signals direction. Each compiles clean and includes unit tests for the directory-prefix logic.

Variant A — match scp -r semantics by default (breaking)
Branch: fix/sandbox-upload-preserve-dir-default
Diff: main...mjamiv:OpenShell:fix/sandbox-upload-preserve-dir-default

Single-file change to crates/openshell-cli/src/ssh.rs. Always wraps a directory's contents under the source basename. Paths without a meaningful basename (., /) preserve the legacy flat extraction. Tests cover both branches.

Variant B — opt-in --preserve-dir flag (non-breaking)
Branch: feat/sandbox-upload-preserve-dir-flag
Diff: main...mjamiv:OpenShell:feat/sandbox-upload-preserve-dir-flag

Adds preserve_dir_name: bool parameter to sandbox_sync_up (with false for backward compat at non-CLI call sites), wires --preserve-dir into the Upload command, and updates the command help to call out the default-flatten behavior so operators discover the flag without a production incident first.

Variant A is what I'd reach for personally — the breaking change is small (one release-note line) and the current behavior is a quiet footgun. Variant B is the safer option if backward compatibility weighs heavier. Happy to open whichever you prefer as a PR; reply with the variant name and I'll mark it ready for review.

[mjamiv]

Heads-up for triage: the body has been edited from H2 (## ) to H3 (### ) headers so the agent diagnostic section now matches the regex at .github/workflows/issue-triage.yml:26. The bot's only complaint was header level — the diagnostic content was substantive on first filing. Safe to drop the state:triage-needed label on review.