docs: add paper citations, fix pedagogical issues, improve SKILL.md

- Cite arxiv 2602.23922 (Invariant-Driven Automated Testing) in all major docs
- Add Progressive Complexity section to SKILL.md for LLM guidance
- Fix SKILL.md Fast Start example to use deterministic ID generation
- Fix getting-started.md failure output inconsistency
- Fix auth-patterns.md TypeScript syntax in JS doc
- Fix fastify-structure.md Date.now() in test helper
- Fix observe.md misleading workspace heading
- Build: clean | Tests: 849 pass, 0 fail

docs/fastify-structure.md

@@ -374,8 +374,10 @@ import { mkdirSync, rmSync } from 'fs'
 import { tmpdir } from 'os'
 import { join } from 'path'
 
+let testCounter = 0
+
 export function createTestWorkspace() {
-  const dir = join(tmpdir(), `apophis-test-${Date.now()}`)
+  const dir = join(tmpdir(), `apophis-test-${++testCounter}`)
   mkdirSync(dir, { recursive: true })
 
   return {