`setup-state.json` lookup ignores `agentsDir` userConfig

[cofin]

Background

PR #54 wired userConfig.agentsDir into hooks/detect-env.{sh,ps1} so the configured directory is used as the default root when no project state is recorded. However, the lookup for setup-state.json is still hardcoded:

• hooks/detect-env.sh (around detect_project_root): if [[ -f ".agents/setup-state.json" ]]; then ...
• hooks/detect-env.ps1 (Get-FlowRoot): $setupStateFile = ".agents/setup-state.json"

This means: if a user installs with agentsDir=specs, Flow may write its state file to specs/setup-state.json (or wherever the setup flow places it for that user), but detect-env will only ever look in .agents/. Result: the user's configured root is silently ignored on every SessionStart after the first init, and the script falls back to the (now-correct) default fallback path — which masks the problem rather than surfacing it.

Scope

1. Confirm where setup-state.json actually gets written when agentsDir != ".agents" (likely ${agentsDir}/setup-state.json based on flow-setup conventions, but verify).
2. Update detect_project_root (sh) and Get-FlowRoot (ps1) to look in ${DEFAULT_ROOT_DIR}/setup-state.json first, with .agents/setup-state.json retained as a backwards-compat fallback for projects initialized before the agentsDir toggle existed.
3. If the recorded root_directory inside setup-state.json ever conflicts with the env-var-driven agentsDir, decide precedence (project state should still win — that's likely correct — but the decision should be explicit, not accidental).

Acceptance criteria

• With CLAUDE_PLUGIN_OPTION_AGENTSDIR=specs set and specs/setup-state.json present, SessionStart reports Flow Root: specs (not the "(default)" fallback).
• Existing projects with .agents/setup-state.json still resolve correctly when no agentsDir is configured.
• PowerShell parity.

Related

• fix(plugin): valid userConfig schema and wire useBeads/agentsDir into hooks #54 (introduced the gap)
• Gate direct bd calls in commands/skills on useBeads userConfig #53 (parallel follow-up: gate bd in commands/skills on useBeads)

[cofin]

Resolved on main by #59 (agentsDir lookup, building on #54). hooks/detect-env.sh (detect_project_root) and hooks/detect-env.ps1 (Get-FlowRoot) now read ${DEFAULT_ROOT_DIR}/setup-state.json first, with .agents/setup-state.json as a backward-compat fallback.

Acceptance criteria verified:

• ✅ AC1: CLAUDE_PLUGIN_OPTION_AGENTSDIR=specs + specs/setup-state.json → SessionStart reports Flow Root: specs (no (default)).
• ✅ AC2: existing .agents/setup-state.json still resolves when no agentsDir is set.
• ✅ AC3: PowerShell parity (detect-env.ps1 lines 41, 45-46).

Closing as already fixed (not part of #65).