diff --git a/KNOWN-ISSUES.md b/KNOWN-ISSUES.md
index d322d638c..65d00bb2b 100644
--- a/KNOWN-ISSUES.md
+++ b/KNOWN-ISSUES.md
@@ -84,6 +84,36 @@ km search 'content:"user:password"'
 
 ---
 
+## Configuration Limitations
+
+### 4. Index ID Hardcoded
+
+**Status:** Known limitation
+
+**Issue:** Index ID is hardcoded as `"fts-main"` instead of being loaded from configuration.
+
+**Location:** `src/Core/Search/NodeSearchService.cs:77`
+
+**Impact:** Cannot configure multiple indexes per node.
+
+**Fix Required:** Load index configuration from node settings.
+
+---
+
+### 5. Index Weights Not Configurable
+
+**Status:** Known limitation
+
+**Issue:** Index weights for reranking use hardcoded defaults instead of configuration.
+
+**Location:** `src/Core/Search/SearchService.cs:223`
+
+**Impact:** Cannot tune relevance scoring per index.
+
+**Fix Required:** Load index weights from configuration file.
+
+---
+
 ## Testing Gaps
 
 These bugs were discovered through comprehensive E2E testing. Previous tests only verified:
diff --git a/clean.sh b/clean.sh
index ad7170f24..86ad59770 100755
--- a/clean.sh
+++ b/clean.sh
@@ -13,4 +13,10 @@ rm -rf src/Core/obj
 rm -rf src/Main/bin
 rm -rf src/Main/obj
 
+rm -rf tests/Core.Tests/bin
+rm -rf tests/Core.Tests/obj
 rm -rf tests/Core.Tests/TestResults
+
+rm -rf tests/Main.Tests/bin
+rm -rf tests/Main.Tests/obj
+rm -rf tests/Main.Tests/TestResults
diff --git a/km.sh b/km.sh
index 6c068c184..13487d790 100755
--- a/km.sh
+++ b/km.sh
@@ -1,2 +1,2 @@
-#!/bin/bash
+#!/usr/bin/env bash
 dotnet run --project src/Main/Main.csproj -- "$@"