feat: implemented external thinking flags and transport reasoning controls

- Added the `--external-thinking` CLI flag alongside model capability checks to gate external thinking tool availability.
- Updated Anthropic and Google transports to honor `forceReasoningOff` for native thinking-off controls.
- Renamed the `thoughts` property and parameter to `notes` across think fixtures, tools, and tests.
- Updated system prompt instructions and test suites to verify transport-specific thinking and tool activation.

packages/coding-agent/test/flag-tables.test.ts

@@ -56,6 +56,18 @@ describe("OPTIONAL_VALUE_FLAGS table is honored by args.ts parseArgs", () => {
 	}
 });
 
+describe("--external-thinking", () => {
+	it("enables external thinking without consuming the initial message", () => {
+		const result = parseArgs(["--external-thinking", "check this"]);
+
+		expect(result.externalThinking).toBe(true);
+		expect(result.messages).toEqual(["check this"]);
+	});
+
+	it("stays unset when omitted", () => {
+		expect(parseArgs([]).externalThinking).toBeUndefined();
+	});
+});
 describe("--session-dir", () => {
 	it("uses PI_CODING_AGENT_SESSION_DIR unless the CLI flag overrides it", () => {
 		const previous = Bun.env.PI_CODING_AGENT_SESSION_DIR;