refactor: runtime isolation — deprecate global singletons, add counter resets

config.ts: @deprecated on configure/getConfig/project/getProjectConfig.
  Current code has zero production callers — dead code path. Functions
  remain for backward compatibility but signal migration to scoped config.

context.ts: @deprecated on setDefaultContext. Documents that consumers
  should call resetDefaultContext() after use in tests to prevent
  context-seed leakage.

pipeline.ts: Export resetTraceCounter() for test isolation of _traceId
  counter variable.

extraction.ts: Export resetPageCacheNamespaceCounter() for test
  isolation of pageCacheNamespaceCounter.

Combined with prior fix (defaultPredicatesRegistered→sentinel check
+ compatibilityWarningEmitted→warnedUis WeakSet), 5 of 7 correctness-
  affecting global mutable state items are now tied down. Remaining:
  globalPredicateRegistry/globalClauseRegistry (already @deprecated
  with explicit injection path via LogicEngineOptions/EvalOptions).

605 SDK + 57 E2E = 662 tests pass.

packages/imhotep-core/src/context.ts

@@ -119,12 +119,12 @@ export function getDefaultContext(): ExecutionContext {
   return _defaultContext
 }
 
-/** Set the global default context (useful for test setup). */
+/** @deprecated Prefer explicit context injection. Sets the global mutable default context. */
 export function setDefaultContext(ctx: ExecutionContext): void {
   _defaultContext = ctx
 }
 
-/** Reset the global default context so the next call creates a fresh one. */
+/** Reset the global default context. Call after using setDefaultContext() in tests. */
 export function resetDefaultContext(): void {
   _defaultContext = undefined
 }

packages/imhotep-core/src/pipeline.ts

@@ -457,10 +457,16 @@ CODE_TO_CLAUSE_KIND[15] = 'size.aspectRatio'
 // ---------------------------------------------------------------------------
 
 let _traceId = 0
+
 function nextTraceId(): string {
   return `trace_${++_traceId}`
 }
 
+/** Reset the trace ID counter (for test isolation). */
+export function resetTraceCounter(): void {
+  _traceId = 0
+}
+
 function now(): number {
   return Date.now()
 }