Support branch_prefix in github-app.yml, mirroring the Project Settings override

## Summary

The per-project "Branch prefix override" setting (Project Settings → Branch prefix override, screenshot below) currently only lives in the app's local SQLite state (`projects.branch_prefix`) and must be set manually, per machine, through the UI. Please add a `branch_prefix` field to `.github/github-app.yml` so it can be version-controlled and shared automatically across a team, consistent with how `instructions`, `server_ready_pattern`, and `auto_open_in_browser` already work in that file.

## Current behavior

- Project Settings has a working "Branch prefix override" toggle + text field (supports `%username%`/similar placeholders, e.g. `%dat%-` → preview `%dat%-my-feature`).
- This setting is local-only: it lives in the per-user `~/.copilot/data.db` (`projects.branch_prefix` column) and has to be re-entered by every teammate, on every machine, for every clone of the project.
- `.github/github-app.yml` already supports several per-repo settings that mirror Project Settings fields 1:1 (`instructions`, `server_ready_pattern`, `auto_open_in_browser`, `automation.*`), but not `branch_prefix`.

## Proposed change

Add an optional `branch_prefix` field to the `github-app.yml` schema, e.g.:

```yaml
branch_prefix: "copilot-"
```

Behavior should match the existing UI field:
- Supports the same placeholder syntax (e.g. `%username%`).
- An explicit empty string (`branch_prefix: ""`) disables any prefix, matching the existing 3-state semantics already implemented for `projects.branch_prefix` (`NULL` = inherit global default, `""` = explicitly disabled, non-empty = literal override).
- Since this file already goes through a user trust/approval prompt before any of its settings are applied (per the existing `accept_repo_config`/`revoke_repo_config` flow), this fits naturally into the same trust model — no new security surface needed.

If it conflicts with the local per-project UI override, the more specific/most-recently-set value should probably win, or the UI field could simply be treated as read-only display of the effective value when set via config-as-code (whichever is simplest to reason about).

## Why this matters

Related open requests confirm real demand for consistent, shareable branch naming across a team:

- #363 — configurable prefix + context-derived branch slugs
- #1344 — branch renames getting "stuck" after the first rename
- #579 — custom worktree/branch naming at session creation

None of these solve the "make it consistent for my whole team without everyone manually configuring their own app" problem — which `github-app.yml` is exactly the right mechanism for, since it's already the config-as-code surface for other per-repo settings.

## Additional context

Filed after reverse-engineering the `github-app.yml` schema for #83 (doc gap) — happy to share findings on the current schema if useful for scoping this.

Start with the `.github/github-app.yml` schema and the existing handling for `instructions`, `server_ready_pattern`, and `auto_open_in_browser`. Trace how `accept_repo_config`/`revoke_repo_config` applies trusted settings and how `projects.branch_prefix` is read by Project Settings. Done means an optional `branch_prefix` supports placeholders and explicit empty values without bypassing the existing trust flow, with the local-versus-config precedence defined and covered by tests.

Written by the indexing model from the issue text.