feat(run): allow passing Octokit and log (#1984)

docs/development.md

@@ -166,6 +166,20 @@ import app from "./index.js";
 run(app);
 ```
 
+You can also set your own [`Octokit` constructor](https://github.com/octokit/core.js) with custom plugins and a custom logger while still reading default options from `.env`:
+
+```js
+// main.js
+import { run } from "probot";
+import app from "./index.js";
+
+// pass a probot app function by overriding Probot options
+run(app, {
+  Octokit: ProbotOctokit.plugin(myPlugin),
+  log: pino(),
+});
+```
+
 Now you can run `main.js` however you want.
 
 ### Use server
@@ -175,7 +189,7 @@ The [`run`](https://github.com/probot/probot/blob/master/src/run.ts) function th
 1. Read configuration from environment variables and local files
 2. Start a [`Server`](https://probot.github.io/api/latest/classes/server_server.Server.html) instance
 
-Among other things, using the Server instance permits you to set your own [`Octokit` constructor](https://github.com/octokit/core.js) with custom plugins and a custom logger.
+If you need more control over the Server instance, you can use the `Server` class directly:
 
 ```js
 import { Server, Probot } from "probot";

src/run.ts

@@ -1,7 +1,7 @@
 import pkgConf from "pkg-conf";
 
 import type { ApplicationFunction, Options, ServerOptions } from "./types.js";
-import { Probot } from "./index.js";
+import { Logger, Probot, ProbotOctokit } from "./index.js";
 import { setupAppFactory } from "./apps/setup.js";
 import { getLog } from "./helpers/get-log.js";
 import { readCliOptions } from "./bin/read-cli-options.js";
@@ -13,7 +13,9 @@ import { isProduction } from "./helpers/is-production.js";
 import { config as dotenvConfig } from "dotenv";
 
 type AdditionalOptions = {
-  env: NodeJS.ProcessEnv;
+  env?: NodeJS.ProcessEnv;
+  Octokit?: typeof ProbotOctokit;
+  log?: Logger;
 };
 
 /**
@@ -70,7 +72,8 @@ export async function run(
     redisConfig,
     secret,
     baseUrl,
-    log: log.child({ name: "probot" }),
+    log: additionalOptions?.log || log.child({ name: "probot" }),
+    Octokit: additionalOptions?.Octokit || undefined,
   };
 
   const serverOptions: ServerOptions = {