Initialize repository with harness code and assets

Initial import of all source code, config, and README assets: the
packages workspace (cli, core, server, web, docs, landing, skills),
build scripts, tooling config, and CI workflows.

Includes the data-layout revision made on this branch: the local data
root defaults to ~/.penguin/data (PENGUIN_HOME still overrides; the
installer keeps its binaries in ~/.penguin), and every Agent lives
under <project>/agents/<agent>/ — path helpers, the three
agent-enumeration scans, the system prompt, built-in Skills, tests
and docs all follow the new layout.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_018ihk8iQuo3kv2aPjAYEPuR

packages/core/src/llm/index.ts

@@ -0,0 +1,22 @@
+/**
+ * LLM interface module entry point.
+ *
+ * Exports `GenerativeModel` (the LLMInterface implementation), along with internal
+ * pure conversion functions for unit testing (message merging, event translation,
+ * token accounting, UniConfig construction, retry determination).
+ */
+export {
+  GenerativeModel,
+  EventTranslator,
+  groupHistoryToUniMessages,
+  mergeOmniToUniMessage,
+  translateEvents,
+  usageToTokenCounts,
+  isMalformedJsonParseError,
+  isIncompleteStreamError,
+  isRetryableError,
+  mapThinkingLevel,
+  toolDefinitionsToSchemas,
+  buildUniConfig,
+} from "./generative-model.js";
+export { ToolCallIdAllocator, stripToolCallIdSuffix } from "./tool-call-ids.js";

packages/core/src/llm/tool-call-ids.ts

@@ -0,0 +1,51 @@
+/**
+ * Session-level uniqueness for tool_call_id.
+ *
+ * Some providers don't produce a real call id: e.g. Gemini's functionCall has no id, so AgentHub
+ * uses the **function name** as the `tool_call_id` — consecutive/parallel calls to the same tool then
+ * all share one id. But the OmniMessage world (engine dispatch/pairing, approval routing, frontend
+ * tool-card attribution) keys on `tool_call_id`, and a collision lets a later call overwrite the
+ * earlier one (parallel same-name calls in one turn can even be dropped entirely).
+ *
+ * Approach: inbound, `EventTranslator` disambiguates duplicate ids with a `#n` suffix (the first keeps
+ * the original id); outbound (returning tool_result, replaying history on resume) uses
+ * `stripToolCallIdSuffix` to strip the suffix and restore the original — Gemini's functionResponse
+ * pairs by using `tool_call_id` as the name, so it must be restored to the function name. The registry
+ * lives at Session level (the new GenerativeModel rebuilt on compaction shares the same instance), and
+ * on resume `setHistory` seeds it with historical ids, so the uniqueness scope covers the entire
+ * context the frontend renders.
+ * Docs: /docs/interfaces § "The built-in implementation: GenerativeModel".
+ */
+export class ToolCallIdAllocator {
+  /** OmniMessage-level tool_call_ids already taken in this Session (history-seeded + allocated). */
+  private used = new Set<string>();
+
+  /** Register an already-used id (for resume seeding); registering twice is harmless. */
+  markUsed(id: string): void {
+    this.used.add(id);
+  }
+
+  /**
+   * Allocate a Session-unique id for a provider-reported tool_call_id: if unused, keep the original;
+   * if already used (a repeat call from a name-as-id provider), take the first free `origId#n` (n from 2).
+   * Providers with truly unique ids (OpenAI `call_*` / Claude `toolu_*`) never collide, so they pass through unchanged.
+   */
+  allocate(providerId: string): string {
+    let id = providerId;
+    for (let n = 2; this.used.has(id); n += 1) {
+      id = `${providerId}#${n}`;
+    }
+    this.used.add(id);
+    return id;
+  }
+}
+
+/**
+ * Strip the `#n` suffix added by `allocate`, restoring the provider's original id (returns as-is when
+ * there's no suffix; idempotent). On resume there's no registry to compare against, so it trims by
+ * shape: real ids from known providers (OpenAI/Claude `call_*`/`toolu_*`, Gemini function names — `#`
+ * isn't a valid function-name char) never end in `#<digits>`, so they aren't harmed.
+ */
+export function stripToolCallIdSuffix(id: string): string {
+  return id.replace(/#\d+$/, "");
+}