goose `goose configure` Documentation incorrectly references config.yaml instead of config directory

The documentation currently references config.yaml as if it's the only configuration file, but goose actually uses multiple configuration files within the ~/.config/goose/ directory. The documentation should be updated to accurately reflect this multi-file structure.

Current Problem

Documentation references like:

"edit it directly at ~/.config/goose/config.yaml"
"your config file at ~/.config/goose/config.yaml"
Instructions to modify config.yaml for settings that are actually stored elsewhere

Expected Behavior

Documentation should:

Reference the config directory (~/.config/goose/) when discussing configuration generally
Specify which specific file is used for different types of configuration
Explain the purpose of each configuration file

Configuration Files Structure

~/.config/goose/
├── config.yaml              # Provider, model, extensions, general settings
├── permission.yaml          # Tool permission levels (user-configured)
├── secrets.yaml             # Secrets (when keyring is disabled)
└── permissions/             # Runtime permission decisions (auto-managed)
    └── tool_permissions.json

Files That Need Updates

The following 13 documentation files reference config.yaml and need to be reviewed and updated:

High Priority

documentation/docs/guides/config-file.md - Main config documentation
documentation/docs/getting-started/installation.md
documentation/docs/troubleshooting.md

Medium Priority

documentation/docs/getting-started/using-extensions.md
documentation/docs/guides/managing-tools/tool-router.md
documentation/docs/guides/subagents.mdx
documentation/docs/guides/recipes/session-recipes.md
documentation/docs/guides/multi-model/creating-plans.md
documentation/docs/guides/multi-model/autopilot.md
documentation/docs/guides/sessions/smart-context-management.md

Lower Priority

documentation/docs/tutorials/isolated-development-environments.md
documentation/docs/tutorials/cicd.md
documentation/blog/2025-06-19-isolated-development-environments/index.md

Suggested Changes

General References

Before:

You can edit your config file at `~/.config/goose/config.yaml`

After:

Configuration files are stored in `~/.config/goose/`. The main config file is `config.yaml`.

Specific Settings

When documenting specific settings, specify which file:

Example for provider settings:

Provider and model settings are stored in `~/.config/goose/config.yaml`

Example for permissions:

Tool permissions are stored in `~/.config/goose/permission.yaml`

Add Configuration Overview Section

The main config documentation (docs/guides/config-file.md) should include a section explaining all configuration files:

## Configuration Files

goose stores configuration in multiple files within `~/.config/goose/`:

- **config.yaml** - Provider, model, extensions, and general settings
- **permission.yaml** - Tool permission levels configured via `goose configure`
- **secrets.yaml** - API keys and secrets (only when keyring is disabled)
- **permissions/tool_permissions.json** - Runtime permission decisions (auto-managed)

Related Issue

This is part of the fix for the bug reported in #4734, which identified that goose misdocuments its configuration structure. The CLI portion is being addressed in a separate issue.

Acceptance Criteria

[ ] All 13 documentation files have been reviewed
[ ] References to config.yaml are updated to either:
- Reference the config directory generally, OR
- Specify the correct file for the specific setting
[ ] Main config documentation includes overview of all config files
[ ] Documentation accurately reflects which settings go in which files
[ ] No misleading references that suggest only config.yaml is used