Fix sync skipping directory spec_paths

[coherent-cache]

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 the directory resolution bug described below. See also issue #3 for a second related bug (DuckDB version compatibility).

Problem

When spec_paths in .plumb/config.json contains a directory (e.g., "specs/"), sync_decisions() silently skips all spec files because spec_path.is_file() returns False for directories. The same bug exists in _run_modify() in cli.py.

This means plumb sync reports "No unsynced decisions found" or syncs 0 spec sections even when there are approved decisions waiting — the decisions get marked as synced but spec files are never updated.

parse_spec_files() in the same file already handles directories correctly by expanding them via rglob("*.md"). The inconsistency is between these two functions in sync.py:

# parse_spec_files — WORKS (resolves directories)
for spec_path_str in config.spec_paths:
    spec_path = repo_root / spec_path_str
    if spec_path.is_dir():
        md_files = list(spec_path.rglob("*.md"))
    elif spec_path.is_file():
        md_files = [spec_path]

# sync_decisions — BROKEN (skips directories)
for spec_path_str in config.spec_paths:
    spec_path = repo_root / spec_path_str
    if not spec_path.is_file():  # ← False for directories, skips everything
        continue

Fix

Apply the same directory resolution pattern from parse_spec_files to:

• sync_decisions() in sync.py
• _run_modify() in cli.py

Tests

• Added initialized_repo_dir_specs fixture with spec_paths: ["specs/"]
• test_syncs_when_spec_path_is_directory — verifies sync_decisions calls the updater for each .md file found in the directory
• test_parses_spec_files_from_directory — verifies parse_spec_files finds files inside directory spec_paths

All 19 sync tests pass.