sync_decisions silently fails with directory spec_paths + DuckDB <1.0 compatibility

[coherent-cache]

Two bugs that cause plumb sync to silently fail

Context

I'm using plumb alongside spec-kit for a spec-driven development workflow. spec-kit generates feature specs under a specs/ directory (e.g., specs/001-feature/spec.md, specs/002-feature/spec.md), so the natural plumb config is:

{
  "spec_paths": ["specs/"]
}

This triggers both bugs below.

Bug 1: Directory spec_paths skipped in sync_decisions (PR #2)

When spec_paths contains a directory (e.g., "specs/"), sync_decisions() in sync.py and _run_modify() in cli.py skip it because spec_path.is_file() returns False. Meanwhile, parse_spec_files() in the same file handles directories correctly via rglob("*.md").

Impact: plumb sync marks decisions as synced but never updates any spec files. The user sees "0 spec sections updated" with no error.

Fix: PR #2 applies the same directory resolution pattern to both functions.

Bug 2: read_all_decisions() fails silently with DuckDB <1.0

decision_log.py line 161 uses format='newline_delimited' in the DuckDB query:

FROM read_json_auto('{glob_pattern}', format='newline_delimited')

DuckDB versions before ~1.0 don't support the format parameter (the parameter was called json_format in older versions, or didn't exist). The query fails, the exception is caught on line 173 (except Exception: return []), and read_all_decisions() silently returns an empty list.

Impact: All commands that use read_all_decisions() — including plumb sync, plumb status, and plumb coverage — see zero decisions. plumb sync reports "No unsynced decisions found."

Workaround: pip install --upgrade duckdb (upgrade to ≥1.0). I upgraded from 0.7.1 → 1.5.0.

Suggested fix: Either pin duckdb>=1.0 in setup.cfg/pyproject.toml, or add a fallback query without the format parameter for older versions. Also consider not silently swallowing the exception — at minimum log it so users can diagnose the failure.

Combined effect

With both bugs present, plumb sync appears to work but does nothing:

1. Bug 2 makes read_all_decisions() return [] → "No unsynced decisions"
2. Even after fixing DuckDB, Bug 1 makes the spec file loop skip all files → "0 spec sections updated" but decisions get marked as synced

Environment: macOS, Python 3.11, plumb 0.2.4, DuckDB 0.7.1 (before upgrade)