fix(hooks): dedupe native agent instructions

src/hooks/directory-agents-injector/injector.ts

@@ -8,6 +8,137 @@ import { loadInjectedPaths, saveInjectedPaths } from "./storage";
 
 type DynamicTruncator = ReturnType<typeof createDynamicTruncator>;
 
+const ADDITIONAL_INSTRUCTIONS_MARKER = "Additional project instructions matched for ";
+const DIRECTORY_CONTEXT_MARKER = "[Directory Context: ";
+const INSTRUCTIONS_FROM_MARKER = "Instructions from: ";
+
+interface InstructionBlock {
+  path: string;
+  start: number;
+  end: number;
+  source: "directory-context" | "instructions-from";
+}
+
+function lineStartAt(output: string, index: number): number {
+  const previousNewline = output.lastIndexOf("\n", index - 1);
+  return previousNewline === -1 ? 0 : previousNewline + 1;
+}
+
+function lineEndAt(output: string, index: number): number {
+  const nextNewline = output.indexOf("\n", index);
+  return nextNewline === -1 ? output.length : nextNewline;
+}
+
+function findAdditionalInstructionsBlockStart(output: string, instructionsLineStart: number): number {
+  const headerStart = output.lastIndexOf(ADDITIONAL_INSTRUCTIONS_MARKER, instructionsLineStart);
+  if (headerStart === -1) return instructionsLineStart;
+
+  const headerLineEnd = lineEndAt(output, headerStart);
+  if (headerLineEnd > instructionsLineStart) return instructionsLineStart;
+
+  const gap = output.slice(headerLineEnd, instructionsLineStart);
+  return gap.trim() === "" ? headerStart : instructionsLineStart;
+}
+
+function findNextInstructionBlockStart(output: string, from: number): number {
+  const markers = [
+    `\n\n${ADDITIONAL_INSTRUCTIONS_MARKER}`,
+    `\n\n${DIRECTORY_CONTEXT_MARKER}`,
+    `\n\n${INSTRUCTIONS_FROM_MARKER}`,
+  ];
+  const starts = markers
+    .map((marker) => output.indexOf(marker, from))
+    .filter((index) => index !== -1);
+  return starts.length > 0 ? Math.min(...starts) : output.length;
+}
+
+function collectInstructionBlocks(output: string): InstructionBlock[] {
+  const blocks: InstructionBlock[] = [];
+
+  let searchIndex = 0;
+  while (true) {
+    const markerIndex = output.indexOf(INSTRUCTIONS_FROM_MARKER, searchIndex);
+    if (markerIndex === -1) break;
+
+    const lineStart = lineStartAt(output, markerIndex);
+    const lineEnd = lineEndAt(output, markerIndex);
+    const instructionPath = output.slice(markerIndex + INSTRUCTIONS_FROM_MARKER.length, lineEnd).trim();
+    if (instructionPath) {
+      blocks.push({
+        path: instructionPath,
+        start: findAdditionalInstructionsBlockStart(output, lineStart),
+        end: findNextInstructionBlockStart(output, lineEnd),
+        source: "instructions-from",
+      });
+    }
+    searchIndex = lineEnd;
+  }
+
+  searchIndex = 0;
+  while (true) {
+    const markerIndex = output.indexOf(DIRECTORY_CONTEXT_MARKER, searchIndex);
+    if (markerIndex === -1) break;
+
+    const pathStart = markerIndex + DIRECTORY_CONTEXT_MARKER.length;
+    const pathEnd = output.indexOf("]", pathStart);
+    if (pathEnd === -1) break;
+
+    const instructionPath = output.slice(pathStart, pathEnd).trim();
+    if (instructionPath) {
+      blocks.push({
+        path: instructionPath,
+        start: lineStartAt(output, markerIndex),
+        end: findNextInstructionBlockStart(output, pathEnd),
+        source: "directory-context",
+      });
+    }
+    searchIndex = pathEnd + 1;
+  }
+
+  return blocks.sort((a, b) => a.start - b.start);
+}
+
+function removeInstructionBlockRanges(
+  output: string,
+  ranges: Array<{ start: number; end: number }>,
+): string {
+  let deduped = output;
+  for (const range of [...ranges].sort((a, b) => b.start - a.start)) {
+    deduped = deduped.slice(0, range.start) + deduped.slice(range.end);
+  }
+  return deduped.replace(/\n{3,}/g, "\n\n").replace(/\n+$/, "");
+}
+
+function dedupeExistingInstructionBlocks(
+  output: string,
+  cache: Set<string>,
+): { output: string; dirty: boolean } {
+  const blocks = collectInstructionBlocks(output);
+  if (blocks.length === 0) return { output, dirty: false };
+
+  const seenInOutput = new Set<string>();
+  const rangesToRemove: Array<{ start: number; end: number }> = [];
+  let dirty = false;
+
+  for (const block of blocks) {
+    const repeatedNativeInstruction = block.source === "instructions-from" && cache.has(block.path);
+    if (repeatedNativeInstruction || seenInOutput.has(block.path)) {
+      rangesToRemove.push({ start: block.start, end: block.end });
+      dirty = true;
+      continue;
+    }
+
+    cache.add(block.path);
+    seenInOutput.add(block.path);
+    dirty = true;
+  }
+
+  return {
+    output: rangesToRemove.length > 0 ? removeInstructionBlockRanges(output, rangesToRemove) : output,
+    dirty,
+  };
+}
+
 function getSessionCache(
   sessionCaches: Map<string, Set<string>>,
   sessionID: string,
@@ -36,15 +167,17 @@ export async function processFilePathForAgentsInjection(input: {
   const dir = dirname(resolved);
   const cache = getSessionCache(input.sessionCaches, input.sessionID);
   const agentsPaths = await findAgentsMdUp({ startDir: dir, rootDir: input.ctx.directory });
+  const dedupedExisting = dedupeExistingInstructionBlocks(input.output.output, cache);
+  input.output.output = dedupedExisting.output;
 
-  let dirty = false;
+  let dirty = dedupedExisting.dirty;
   for (const agentsPath of agentsPaths) {
     const agentsDir = dirname(agentsPath);
-    if (cache.has(agentsDir)) continue;
+    if (cache.has(agentsPath) || cache.has(agentsDir)) continue;
 
     try {
       const content = await fsPromises.readFile(agentsPath, "utf-8");
-      cache.add(agentsDir);
+      cache.add(agentsPath);
       const { result, truncated } = await input.truncator.truncate(
         input.sessionID,
         content,