feat(init): support configurable scan roots and flexible directory structures

[BalduinLandolt]

Summary

The loom init wizard should allow configuring the repository scan root during setup, and LOOM should support directory structures beyond the current <root>/<org>/<repo> convention.

Motivation

Currently, loom init does not let you choose where to scan for repositories — you have to manually edit config.toml afterward to set scan_roots. This defeats the purpose of having an interactive setup wizard.

More fundamentally, LOOM requires repositories to be organized as <root>/<org>/<repo> (e.g., ~/repos/dasch-swiss/dsp-api). Many developers keep a flat layout like ~/repos/dsp-api. Adopting LOOM currently means reorganizing your entire directory structure, which is a significant barrier to adoption.

Commands affected

• loom init
• loom new
• loom add
• loom remove
• loom down
• loom list
• loom status
• loom exec
• loom shell
• loom save
• loom open
• loom registry
• TUI
• New command

Modules affected

• config
• manifest
• workspace
• git
• agent
• sync
• tui
• registry
• cli

Proposed behavior

1. Wizard scan root prompt: loom init should ask where to scan for repositories, rather than using a hardcoded default.
2. Flexible directory structures: LOOM should support discovering repos in flat directories (<root>/<repo>) in addition to the current org-grouped layout (<root>/<org>/<repo>). This could be a config option like scan_depth or layout = "flat" | "org-grouped".

Acceptance criteria

• loom init prompts the user for scan root path(s)
• Flat directory layouts (<root>/<repo>) are supported for repo discovery
• Existing org-grouped layouts continue to work
• No manual config.toml editing required after loom init for basic setup

[subotic]

Closed by #69 — configurable scan_depth (1-4) with tree-based repo selector