diff --git a/scripts/profiles/base-profile.js b/scripts/profiles/base-profile.js
index b39dd38a..abae3c8c 100644
--- a/scripts/profiles/base-profile.js
+++ b/scripts/profiles/base-profile.js
@@ -67,7 +67,7 @@ export function createProfile(editorConfig) {
 		...(targetExtension !== fileExtension
 			? [
 					{
-						from: new RegExp(`\\${fileExtension}\\b`, 'g'),
+						from: new RegExp(`\\${fileExtension}(?!\\])\\b`, 'g'),
 						to: targetExtension
 					}
 				]
@@ -168,7 +168,14 @@ export function createProfile(editorConfig) {
 				const baseName = path.basename(filePath, '.mdc');
 				const newFileName =
 					fileMap[`${baseName}.mdc`] || `${baseName}${targetExtension}`;
-				return `[${text}](mdc:${rulesDir}/${newFileName})`;
+				// Update the link text to match the new filename
+				const newLinkText = newFileName;
+				// For Cursor, keep the mdc: protocol; for others, use standard relative paths
+				if (name.toLowerCase() === 'cursor') {
+					return `[${newLinkText}](mdc:${rulesDir}/${newFileName})`;
+				} else {
+					return `[${newLinkText}](${rulesDir}/${newFileName})`;
+				}
 			}
 		}
 	};
diff --git a/src/utils/rule-transformer.js b/src/utils/rule-transformer.js
index 95bb6200..daab8ef0 100644
--- a/src/utils/rule-transformer.js
+++ b/src/utils/rule-transformer.js
@@ -136,12 +136,12 @@ function transformCursorToProfileRules(
 	conversionConfig,
 	globalReplacements = []
 ) {
-	// Apply all transformations in appropriate order
 	let result = content;
+	// Apply all transformations in appropriate order
+	result = updateFileReferences(result, conversionConfig);
 	result = replaceBasicTerms(result, conversionConfig);
 	result = replaceToolReferences(result, conversionConfig);
 	result = updateDocReferences(result, conversionConfig);
-	result = updateFileReferences(result, conversionConfig);
 
 	// Apply any global/catch-all replacements from the profile
 	// Super aggressive failsafe pass to catch any variations we might have missed