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

mcp/server.ts

@@ -72,6 +72,9 @@ export interface ToolState {
   issueNumber?: number;
   // PR HEAD sha at checkout time — used to detect new commits pushed during a review
   checkoutSha?: string;
+  // SHA to diff incrementally against — set from event payload on first checkout,
+  // then from checkoutSha when review.ts detects new commits mid-review
+  beforeSha?: string;
   selectedMode?: string;
   backgroundProcesses: Map<string, BackgroundProcess>;
   browserDaemon?: BrowserDaemon | undefined;