Add mise setup integration

[codeforester]

Summary

• Add top-level mise: <relative-path> support to base_manifest.yaml.
• Run mise install from the project root during basectl setup when a project declares mise.
• Add check/doctor visibility for mise config path and CLI availability without mutating state.
• Add path guardrails so mise config paths stay relative and inside the project root.
• Update README and architecture docs to describe the implemented setup behavior.

Notes

This PR intentionally does not add basectl test or mise run task delegation. That belongs with #119.

Validation

• PYTHONPATH=lib/python:cli/python ~/.base.d/base/.venv/bin/python -m unittest cli.python.base_setup.tests.test_engine
• bats cli/bash/commands/basectl/tests/setup.bats
• bats cli/bash/commands/basectl/tests/basectl.bats
• git diff --check

Fixes #118