chore: improve project consistency and add pre-commit hook

- Add pre-commit hook that runs format.sh and build.sh
- Update clean.sh to include Main.Tests cleanup
- Add km.sh portable shebang (/usr/bin/env bash)
- Document known configuration limitations in KNOWN-ISSUES.md

Author: dluc

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:

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

km.sh

@@ -1,2 +1,2 @@
-#!/bin/bash
+#!/usr/bin/env bash
 dotnet run --project src/Main/Main.csproj -- "$@"