Rework incremental diffing (#499)

* Improve our deepening logic

* Use consistent SHA for PR-related operations in CheckoutPrTool

* compute `deepenDepth` at more appropriate time

* fix stale comment

* add comments for `alreadyOnBranch`

* ensure before sha is available

* small cleanup

* computeIncrementalDiff

* move the util

* improve algorithm

* improve algorithm further

* get rid of temp result array

* add comment

* compute incremental diff and updte instructions

* add comment

* update stale comment

* get rid of redundant rev-parse call

* improve comment

* strenghten the instructions

* make diff paths unique

main.ts

@@ -172,6 +172,9 @@ export async function main(): Promise<MainResult> {
   // resolve payload to determine shell permission
   const payload = resolvePayload(resolvedPromptInput, runContext.repoSettings);
   toolState.model = payload.model;
+  if (payload.event.trigger === "pull_request_synchronize") {
+    toolState.beforeSha = payload.event.before_sha;
+  }
 
   // resolve tokens first — acquireNewToken needs OIDC env vars for token exchange
   await using tokenRef = await resolveTokens({ push: payload.push });