bug: run workflow ignores brownfield default repo path, uses $HOME as cwd

[kenlin8827]

Bug Description

When running ouroboros run workflow, the opencode runtime is launched with $HOME as the working directory instead of the registered brownfield default repo path.

Steps to Reproduce

1. Register a brownfield repo:

   ouroboros setup scan /path/to/project
   ouroboros setup default  # select the project

2. Verify registration:
   ```bash
     ouroboros setup list
     # Shows: ★ project-name /path/to/project
   ```
3. Run workflow from the project directory:
   ```bash
     cd /path/to/project
     ouroboros run workflow seed.yaml --sequential
   ```
4. Check logs - shows cwd=$HOME instead of /path/to/project

Expected Behavior

opencode should be launched with the brownfield default repo path as cwd:

cwd=/path/to/project

Actual Behavior

opencode is launched with user home directory:

cwd=$HOME

Environment

- OS: Windows
- Ouroboros version: 0.40.1
- Runtime: opencode
- Shell: Git Bash

Impact

- opencode has to search for project files, adding significant startup time
- Execution context is wrong, potentially causing file path issues
- Brownfield registration appears to be metadata-only, not used for execution context

Workaround

None found. Even running from the project directory doesn't help - ouroboros seems to hardcode $HOME as cwd when launching the runtime.

[shaun0927]

Maintainer triage: this is a valid bug, but I think the issue scope should be narrowed/clarified.

Confirmed valid part:

• A seed under the global seed store, ~/.ouroboros/seeds/..., structurally matches the project-local central seed layout, <project>/.ouroboros/seeds/....
• Because of that, _detect_project_root_from_seed_path() can recover Path.home() as the candidate project root.
• That can make the runtime launch with cwd=$HOME, which is wrong for ouroboros run workflow.

Scope clarification:

• I do not think the current SSOT/roadmap contract says ouroboros run workflow must automatically use the DB-registered brownfield default repo from ouroboros setup default as cwd.
• The already accepted run-path fix in bug(run): ouroboros run workflow has no --project-dir; brownfield_context.target_dir ignored (mirror of #594 for run) #1160/fix(run): resolve project dirs for central seeds #1161 established the explicit project-boundary path as --project-dir, raw metadata.project_dir / metadata.working_directory, and brownfield_context.target_dir, with seed-parent/project-local central-seed fallback behavior.
• Therefore this issue is best understood as: global ~/.ouroboros/seeds is misdetected as a project-local central seed, causing cwd=$HOME.

Recommended disposition:

• Keep this open as a real bug.
• Retitle/narrow it away from “registered brownfield default repo must be used” unless we intentionally open a separate design issue for DB default repo cwd semantics.
• A minimal fix should prevent Path.home() from being accepted as a project root for globally stored seeds and should include resolver-level regression coverage.

This sits in the narrow run workflow follow-up lane, not as a new #961 Track C tier-gated AgentOS substrate item.

[ouroboros-agent]

There's already an open PR addressing this: #1313. Review is in progress.

ouroboros-agent[bot]