Extract bootstrap/AppBuilder from main.rs

[bug-ops]

Part of #391

Problem

main() in src/main.rs is a ~2400-line god function annotated with #[allow(clippy::too_many_lines)]. It handles provider creation, channel setup, memory init, skill matching, MCP, indexing, TUI, A2A, config watchers, and agent builder chain.

Proposed Solution

Extract an AppBuilder or Bootstrap struct in zeph-core that encapsulates the initialization sequence. Provider factory (separate issue) belongs in zeph-llm.

Priority: P0 | Effort: Large