refactor: introduce ServerContext and createServer (cppalliance#130)

* added server-context.ts and updated related files

* use disableSuggestFlow

* addressed CI test error

* addressed ai review

* addressed ai reviews

---------

Co-authored-by: zho <jornathanm910923@gmail.com>

Author: jonathanMLDev

docs/MIGRATION.md

@@ -6,6 +6,67 @@ This guide is for **library and MCP client authors** upgrading from earlier **0.
 
 Under [semver 0.y.z](https://semver.org/spec/v2.0.0.html#spec-item-4), **0.1.x → 0.2.0 is a breaking minor** — pin `@0.2.0` only after reading this guide.
 
+## Unreleased: `ServerContext` instance APIs (phase 1)
+
+**Rationale:** Process-global singletons (Pinecone client slot, config, URL registry, suggest-flow gate, namespaces cache) complicate testing and multi-tenant embedding. Phase 1 introduces an opt-in **`ServerContext`** without removing legacy getters.
+
+**Now (0.2.x — unchanged for existing embedders):**
+
+```ts
+import { PineconeClient, setPineconeClient } from '@will-cppa/pinecone-read-only-mcp';
+import {
+  resolveAllianceConfig,
+  setupAllianceServer,
+} from '@will-cppa/pinecone-read-only-mcp/alliance';
+
+const config = resolveAllianceConfig({ apiKey: process.env.PINECONE_API_KEY! });
+setPineconeClient(
+  new PineconeClient({
+    /* ... */
+  })
+);
+const server = await setupAllianceServer(config);
+```
+
+Module-level helpers (`getPineconeClient`, `registerUrlGenerator`, `requireSuggested`, etc.) continue to work; they delegate to a process-default context.
+
+**New (opt-in instance path):**
+
+```ts
+import { createServer, PineconeClient } from '@will-cppa/pinecone-read-only-mcp';
+import {
+  resolveAllianceConfig,
+  setupAllianceServer,
+} from '@will-cppa/pinecone-read-only-mcp/alliance';
+
+const config = resolveAllianceConfig({ apiKey: process.env.PINECONE_API_KEY! });
+const ctx = createServer(config); // installs process-default + returns instance
+ctx.setClient(
+  new PineconeClient({
+    apiKey: config.apiKey,
+    indexName: config.indexName,
+    sparseIndexName: config.sparseIndexName,
+    rerankModel: config.rerankModel,
+    defaultTopK: config.defaultTopK,
+    requestTimeoutMs: config.requestTimeoutMs,
+  })
+);
+const server = await setupAllianceServer(config); // uses process-default ctx for migrated tools
+```
+
+For custom tool wiring, pass `ctx` to migrated registrars:
+
+```ts
+import { registerQueryTool, registerCountTool, registerListNamespacesTool } from '…'; // internal today
+registerQueryTool(server, ctx);
+```
+
+**Later (future minors/major):** Legacy module getters will be marked `### Deprecated` per [deprecation-policy.md](./deprecation-policy.md). Multi-tenant HTTP embedders should use one `ServerContext` per session rather than sharing process-global state.
+
+See also [deprecation-policy.md § Future instance APIs](./deprecation-policy.md#future-instance-apis-servercontext).
+
+---
+
 ## Unreleased: core vs Alliance config defaults
 
 **Rationale:** Generic npm consumers must not silently connect to Alliance infrastructure or inherit Alliance rerank settings when using `resolveConfig` from the package root.
@@ -70,12 +131,12 @@ const ns = userInput.trim();
 
 **`code` values (discriminated union):**
 
-| `code` | `recoverable` | Notes |
-| ------ | --------------- | ----- |
-| `FLOW_GATE` | `true` | Suggestion: call `suggest_query_params` for the namespace first |
-| `VALIDATION` | `true` | **`field` required** — input or `metadata_filter` dot-path |
-| `PINECONE_ERROR` | `true` or `false` | Upstream / network / Pinecone failures |
-| `TIMEOUT` | `true` | Outbound deadline exceeded |
+| `code`           | `recoverable`     | Notes                                                           |
+| ---------------- | ----------------- | --------------------------------------------------------------- |
+| `FLOW_GATE`      | `true`            | Suggestion: call `suggest_query_params` for the namespace first |
+| `VALIDATION`     | `true`            | **`field` required** — input or `metadata_filter` dot-path      |
+| `PINECONE_ERROR` | `true` or `false` | Upstream / network / Pinecone failures                          |
+| `TIMEOUT`        | `true`            | Outbound deadline exceeded                                      |
 
 **Migration steps:**
 
@@ -104,12 +165,12 @@ const ns = userInput.trim();
 
 **Rationale:** Align routing hints with the unified `query` tool vocabulary.
 
-| Old (legacy) | New |
-| ------------ | --- |
-| `query_fast` | `fast` |
-| `query_detailed` | `detailed` |
-| `count` | `count` (unchanged) |
-| _(n/a)_ | `full` (explicit preset) |
+| Old (legacy)     | New                      |
+| ---------------- | ------------------------ |
+| `query_fast`     | `fast`                   |
+| `query_detailed` | `detailed`               |
+| `count`          | `count` (unchanged)      |
+| _(n/a)_          | `full` (explicit preset) |
 
 **Migration steps:**
 
@@ -122,10 +183,10 @@ const ns = userInput.trim();
 
 **Rationale:** One hybrid tool with a `preset` knob instead of duplicate registrations.
 
-| Legacy tool call | New `query` call |
-| ---------------- | ---------------- |
-| `query_fast({ ...params })` | `query({ ...params, preset: 'fast' })` |
-| `query_detailed({ ...params })` | `query({ ...params, preset: 'detailed' })` |
+| Legacy tool call                | New `query` call                                                |
+| ------------------------------- | --------------------------------------------------------------- |
+| `query_fast({ ...params })`     | `query({ ...params, preset: 'fast' })`                          |
+| `query_detailed({ ...params })` | `query({ ...params, preset: 'detailed' })`                      |
 | Custom / explicit rerank+fields | `query({ ...params, preset: 'full', use_reranking?, fields? })` |
 
 **Example:**

docs/deprecation-policy.md

@@ -66,14 +66,14 @@ Security fixes may break behavior when required; document impact in CHANGELOG an
 
 ## Future instance APIs (`ServerContext`)
 
-A planned refactor introduces **`ServerContext`** and **`createServer(config)`** while keeping legacy module-level getters during a transition. That work will:
+Phase 1 of the **`ServerContext`** / **`createServer(config)`** refactor is available while legacy module-level getters remain supported. See [MIGRATION.md § ServerContext instance APIs](./MIGRATION.md#unreleased-servercontext-instance-apis-phase-1) for upgrade steps.
+
+That work will:
 
 - Add new instance APIs without removing legacy getters in the same release.
 - Document legacy getters under `### Deprecated` with a named removal target per this policy.
 - Link migration steps from [MIGRATION.md](./MIGRATION.md) to this document.
 
-Until that migration guide is published, treat this section as the policy constraint for that refactor.
-
 ## CHANGELOG format for breaking changes
 
 This project follows [Keep a Changelog](https://keepachangelog.com/en/1.0.0/). Each version block should use the sections that apply: `### Added`, `### Changed`, `### Deprecated`, `### Removed`, `### Fixed`.

examples/alliance/library-embedding-demo.ts

@@ -3,7 +3,7 @@
  *
  * Pattern (mirrors `src/index.ts`):
  *   1. `resolveAllianceConfig({ apiKey, indexName, ... })` — Alliance index/rerank defaults when unset.
- *   2. `new PineconeClient({ ... })` + `setPineconeClient(client)`.
+ *   2. `new PineconeClient({ ... })` + `setPineconeClient(client)` (legacy), or `createServer(config)` + `ctx.setClient(...)`.
  *   3. `await setupAllianceServer(config)` then `server.connect(transport)`.
  *
  * **Single process:** `setupAllianceServer` registers tools against process-global

src/core/index.ts

@@ -7,6 +7,7 @@
  */
 
 export { setPineconeClient } from './server/client-context.js';
+export { ServerContext, createServer, getDefaultServerContext } from './server/server-context.js';
 export {
   validateMetadataFilter,
   validateMetadataFilterDetailed,

src/core/server/client-context.ts

@@ -1,22 +1,17 @@
 import { PineconeClient } from '../pinecone-client.js';
-
-// Global Pinecone client (initialized lazily)
-let pineconeClient: PineconeClient | null = null;
+import { getDefaultServerContext } from './server-context.js';
 
 /** Return the shared Pinecone client; throws if setPineconeClient has not been called. */
 export function getPineconeClient(): PineconeClient {
-  if (!pineconeClient) {
-    throw new Error('Pinecone client not initialized. Call setPineconeClient first.');
-  }
-  return pineconeClient;
+  return getDefaultServerContext().getClientIfSet();
 }
 
 /** Set the shared Pinecone client used by all MCP tools. */
 export function setPineconeClient(client: PineconeClient): void {
-  pineconeClient = client;
+  getDefaultServerContext().setClient(client);
 }
 
 /** Clear the shared client (used by {@link teardownServer} and tests). */
 export function clearPineconeClient(): void {
-  pineconeClient = null;
+  getDefaultServerContext().clearClient();
 }

src/core/server/config-context.ts

@@ -1,16 +1,18 @@
 import type { ServerConfig } from '../config.js';
-import { resolveConfig } from '../config.js';
-
-let activeConfig: ServerConfig | null = null;
+import {
+  getDefaultServerContext,
+  setDefaultServerContext,
+  setPendingServerConfig,
+} from './server-context.js';
 
 /** Replace the process-global server config (called from setup with CLI/env-derived config). */
 export function setServerConfig(config: ServerConfig): void {
-  activeConfig = config;
+  setPendingServerConfig(config);
 }
 
 /** Clear active config so the next `getServerConfig()` resolves again (used by {@link teardownServer}). */
 export function resetServerConfig(): void {
-  activeConfig = null;
+  setDefaultServerContext(null);
 }
 
 /**
@@ -22,8 +24,5 @@ export function resetServerConfig(): void {
  * pass config from `resolveAllianceConfig()` into `setupAllianceServer(config)`.
  */
 export function getServerConfig(): ServerConfig {
-  if (!activeConfig) {
-    activeConfig = resolveConfig({});
-  }
-  return activeConfig;
+  return getDefaultServerContext().getConfig();
 }

src/core/server/namespaces-cache.ts

@@ -1,18 +1,6 @@
-import { getServerConfig } from './config-context.js';
-import { getPineconeClient } from './client-context.js';
+import { getDefaultServerContext, type NamespaceInfo } from './server-context.js';
 
-export type NamespaceInfo = {
-  namespace: string;
-  recordCount: number;
-  metadata: Record<string, string>;
-};
-
-type CacheEntry = {
-  data: NamespaceInfo[];
-  expiresAt: number;
-};
-
-let namespacesCache: CacheEntry | null = null;
+export type { NamespaceInfo };
 
 /**
  * Return namespace list with metadata; uses an in-memory cache whose TTL is
@@ -23,24 +11,10 @@ export async function getNamespacesWithCache(): Promise<{
   cache_hit: boolean;
   expires_at: number;
 }> {
-  const now = Date.now();
-  if (namespacesCache && now < namespacesCache.expiresAt) {
-    return {
-      data: namespacesCache.data,
-      cache_hit: true,
-      expires_at: namespacesCache.expiresAt,
-    };
-  }
-
-  const client = getPineconeClient();
-  const data = await client.listNamespacesWithMetadata();
-  const ttlMs = getServerConfig().cacheTtlMs;
-  const expiresAt = now + ttlMs;
-  namespacesCache = { data, expiresAt };
-  return { data, cache_hit: false, expires_at: expiresAt };
+  return getDefaultServerContext().getNamespacesWithCache();
 }
 
 /** Clear the namespaces cache so the next call to getNamespacesWithCache refetches. */
 export function invalidateNamespacesCache(): void {
-  namespacesCache = null;
+  getDefaultServerContext().invalidateNamespacesCache();
 }