[Bug] Module detection fails after clean install - commands show as available but don't execute

[danieldekay]

Bug Report: Module Detection Fails After Clean Install

Environment

• SpecFact Version: 0.46.18
• OS: Linux (Ubuntu/Debian)
• Python: 3.12.11
• Installation Method: specfact init --profile solo-developer

Issue Description

After a clean installation, the code command group fails to execute despite modules showing as "enabled" in specfact module list.

Steps to Reproduce

1. Remove existing modules: rm -rf ~/.specfact/modules/
2. Fresh install: specfact init --profile solo-developer
3. Verify installation: specfact module list (shows nold-ai/specfact-codebase as enabled)
4. Try to run command: specfact code --help

Expected Behavior

specfact code --help should display help for code commands.

Actual Behavior

Command produces no output except timing info:

⏱️  Started: 2026-05-06 10:58:23
✓ Finished: 2026-05-06 10:58:23 | Duration: 0.19s

Or sometimes shows error:

Module 'nold-ai/specfact-codebase' is not installed.
The code command group is provided by that module.

Diagnostic Information

Module List Output

$ specfact module list | grep specfact-codebase
│ nold-ai/specfact-codebase    │ 0.41.9  │ enabled │ [official] │ nold-ai   │

Python Import Test

$ python -c "import importlib.util; spec = importlib.util.find_spec('specfact_codebase'); print(spec)"
None  # Module not found in Python path

Module File Structure

$ ls ~/.specfact/modules/specfact-codebase/
src/  # Module code is in src/specfact_codebase/

Root Cause Hypothesis

The modules are installed in ~/.specfact/modules/specfact-codebase/src/, but this path is not being added to sys.path when SpecFact loads modules. Python cannot import specfact_codebase even though the files exist.

Workaround Attempted

• Uninstall + reinstall module: No effect
• Run specfact init multiple times: No effect
• Module shows as enabled but commands don't work

Impact

Cannot use SpecFact codebase import functionality, blocking brownfield code analysis workflow.

Additional Context

• Bootstrap completes successfully: "Modules discovered: 10 (enabled=10, disabled=0)"
• Command indexing completes: "Indexing CLI commands for help cache…"
• Issue persists across multiple clean reinstalls

[djm81]

Source tracking synced: remediation is tracked by user story #557 under feature #353. #557 blocks this bug report until OpenSpec change runtime-01-discovery-reliability is implemented, validated, and merged. Repo decision: stays in nold-ai/specfact-cli, not specfact-cli-modules, because the root cause is CLI runtime module loading/diagnostics.

[djm81]

Implementation tracking update: remediation is tracked through User Story #557, which blocks this bug report. The story now includes a CI-capable runtime discovery smoke script covering installed module discovery and real demo-monorepo validation. This bug remains a source bug report, not a child of the feature/epic.