feat(context): refresh managed instructions per run + additive BEGIN/END managed block

[bradtaylorsf]

Problem

.alpha-loop/templates/instructions.md is synced whole-file into each harness's instruction file — claude → CLAUDE.md, codex/cursor/opencode/gemini/copilot/etc. → AGENTS.md (src/commands/sync.ts:42–82). Two problems:

1. Stale. Instructions/context are generated once at init (often greenfield) and not refreshed as the repo grows. A repo that bootstraps its own stack in epic Setup pnpm, TypeScript, and basic Express server #1 keeps "no source code / stack TBD" guidance for every later epic, actively misleading Plan/Implement.
2. All-or-nothing. sync overwrites a file only if it starts with <!-- managed by alpha-loop --> (sync.ts:9–10), then replaces the entire file. Users can't keep project-specific rules in CLAUDE.md/AGENTS.md alongside managed content — hand-edits are lost on the next sync.

Proposed change

• Re-run scan (or a cheap drift check — e.g. "instructions say no package manager but a lockfile / non-empty packages/ exists") at session start and refresh instructions.md + context.md.
• Replace the whole-file marker with an additive managed block:

  <!-- alpha-loop:begin (managed — do not edit) -->
  …managed content…
  <!-- alpha-loop:end -->
  

  sync replaces only the block; content above/below is preserved. For an unmarked file, append a block (or leave untouched — configurable).

Files

src/lib/context.ts, src/commands/scan.ts, src/commands/sync.ts, src/lib/scan-validation.ts, src/commands/run.ts (drift check at session start).