feat(cli): interactive paths editor, tiered help, and nav (#247)

[rosspeili]

Fixes #247

Interactive CLI UX on top of #246 config: paths submenu with project .skillware.yaml persistence, tiered help, consistent navigation, and small polish on doctor/examples.

Type of Change

• Framework Feature, config.py save helpers, discovery.py tier labels + flat-layout scan
• CLI, paths submenu, tiered help, nav, doctor spinner, examples table
• Documentation, cli.md, README, api_keys.md, ai_native_workflow.md, usage/README.md

Acceptance criteria → implementation

Criterion	Where
Paths submenu wired (menu 4)	skillware/cli.py, cmd_paths_submenu, _PATHS_SUBMENU
Persist project/external, bundled read-only	save_project_config(), submenu options 2–4
Grouped help + doc links	cmd_help_submenu, brief skillware --help index
cli.md + test_cli.py updated	docs + interactive/nav/examples tests

Also in this PR (#246 follow-ups)

• save_project_config() / load_project_paths_settings() in config.py
• Skill-not-found errors show tier: path (discovery.py)
• Universal 0 exit, b back; doctor dots spinner; wider EXTRA / compact GITHUB in skillware examples

Checklist

• Fixes [CLI]: Interactive paths editor and grouped help submenus #247
• black --check / flake8 / pytest (401 passed)
• CHANGELOG.md updated
• examples/README.md, N/A (no script changes)
• test_registry_docs.py, N/A

Test plan

• skillware --help, topic index + CLI usage examples
• Interactive: 4 paths submenu (view, bundled, project, external, shadows, flat)
• Interactive: 6 help topics; 0 / b navigation
• skillware doctor, spinner then DEPS/LOAD table
• skillware examples, EXTRA readable; GITHUB filename link
• save_project_config + tier labels in not-found errors