refactor: extract bootstrap/AppBuilder from main.rs (M24)

[bug-ops]

Summary

Extract initialization logic from the 2300-line main.rs into a structured AppBuilder in zeph-core::bootstrap, reducing main.rs to ~980 lines.

New module: crates/zeph-core/src/bootstrap.rs

AppBuilder provides a structured bootstrap API:

• from_env() — resolve config path, load config, create vault, resolve secrets
• build_provider() — create AnyProvider with health check and context window detection
• build_memory() — SemanticMemory setup with embed_missing backfill
• build_skill_matcher() — Qdrant or in-memory skill matching backend
• build_registry() — SkillRegistry with hot-reload
• build_tool_executor() — CompositeExecutor with shell, scrape, MCP tools
• build_watchers() — skill and config file watchers
• build_shutdown() — graceful shutdown signal handler
• build_summary_provider() — optional summarization provider

What stays in main.rs

• CLI argument parsing (clap)
• Channel creation (AnyChannel dispatch)
• TUI-specific wiring (AppChannel, TuiHandle)
• A2A/Gateway server spawning
• Agent builder chain and run loop

Other changes

• Feature forwarding from root Cargo.toml to zeph-core (candle, compatible, cuda, metal, openai, orchestrator, qdrant, router)
• SecurityConfig and TimeoutConfig gain Clone + Copy

Stats

• 6 files changed, +1777 / -1522
• main.rs: 2313 -> 978 lines
• 1533 tests pass, 0 failures
• Clippy clean, fmt clean

Test plan

• cargo nextest run --workspace --lib --bins --features full,mock (1533 pass)
• cargo clippy --workspace --features full,mock -- -D warnings (clean)
• Code review approved
• CI gate passes

Resolves #393