Harden custom tool builder git and venv flow

[siddsachar]

Summary

Describe what changed and why.

Type of change

• Bug fix
• Feature
• Docs
• Refactor
• Test-only change
• Build / CI / release tooling

Risk area

• Agent / prompts / tools
• Designer
• Memory / knowledge graph
• Channels / external integrations
• Installers / auto-update
• UI only
• Other

Testing

• I ran python tests/test_suite.py
• I added or updated tests
• I manually tested the affected user flow
• Not applicable, docs-only change

Release notes

• User-visible change, release notes needed
• Internal-only change, no release note needed

Checklist

• Branch is based on latest main
• No direct secrets, API keys, local paths, or private data included
• The change is focused and does not include unrelated cleanup
• Windows/macOS behavior considered where relevant