fix: use jsonc-parser for all JSON config files to support comments (#41)

Some clients like opencode use .json files that contain JSONC content (comments). Previously, only .jsonc files were parsed with jsonc-parser, causing JSON.parse() to fail on .json files with comments. This resulted in the entire config being replaced with just the MCP section, losing all other settings.

Now we always use jsonc-parser for reading JSON files and use jsonc.modify() to update only the specific configKey path when writing, preserving comments, formatting, and all other config keys. Indentation is detected from the existing file content so the output matches the original style.

Author: Dhravya

src/client-config.ts

@@ -279,11 +279,10 @@ export function readConfig(client: string, local?: boolean): ClientConfig {
       rawConfig = (yaml.load(fileContent) as ClientConfig) || {}
     } else if (configPath.format === 'toml') {
       rawConfig = TOML.parse(fileContent) as ClientConfig
-    } else if (configPath.path.endsWith('.jsonc')) {
-      // Use jsonc-parser for .jsonc files to support comments
-      rawConfig = jsonc.parse(fileContent) as ClientConfig
     } else {
-      rawConfig = JSON.parse(fileContent)
+      // Always use jsonc-parser for JSON files to support comments
+      // This handles both .json and .jsonc files with comments
+      rawConfig = jsonc.parse(fileContent) as ClientConfig
     }
 
     verbose(`Config loaded successfully: ${JSON.stringify(rawConfig, null, 2)}`)
@@ -319,6 +318,26 @@ export function writeConfig(config: ClientConfig, client?: string, local?: boole
   writeConfigFile(config, configPath)
 }
 
+// Detect indentation style from JSON content using jsonc-parser
+function detectIndent(text: string): { tabSize: number; insertSpaces: boolean } {
+  let result: { tabSize: number; insertSpaces: boolean } | null = null
+
+  jsonc.visit(text, {
+    onObjectProperty: (_property, offset, _length, startLine, startCharacter) => {
+      if (result === null && startLine > 0 && startCharacter > 0) {
+        const lineStart = text.lastIndexOf('\n', offset - 1) + 1
+        const whitespace = text.slice(lineStart, offset)
+        result = {
+          tabSize: startCharacter,
+          insertSpaces: !whitespace.includes('\t'),
+        }
+      }
+    },
+  })
+
+  return result || { tabSize: 2, insertSpaces: true }
+}
+
 // Helper function for deep merge
 function deepMerge(target: ClientConfig, source: ClientConfig): ClientConfig {
   const result = { ...target }
@@ -356,11 +375,9 @@ function writeConfigFile(config: ClientConfig, target: ClientFileTarget): void {
         existingConfig = (yaml.load(originalFileContent) as ClientConfig) || {}
       } else if (target.format === 'toml') {
         existingConfig = TOML.parse(originalFileContent) as ClientConfig
-      } else if (target.path.endsWith('.jsonc')) {
-        // Use jsonc-parser for .jsonc files to support comments
-        existingConfig = jsonc.parse(originalFileContent) as ClientConfig
       } else {
-        existingConfig = JSON.parse(originalFileContent)
+        // Always use jsonc-parser for JSON files to support comments
+        existingConfig = jsonc.parse(originalFileContent) as ClientConfig
       }
 
       verbose(`Existing config loaded: ${JSON.stringify(existingConfig, null, 2)}`)
@@ -385,24 +402,16 @@ function writeConfigFile(config: ClientConfig, target: ClientFileTarget): void {
     })
   } else if (target.format === 'toml') {
     configContent = TOML.stringify(mergedConfig)
-  } else if (target.path.endsWith('.jsonc') && originalFileContent) {
-    // For .jsonc files, try to preserve comments and formatting using jsonc-parser
+  } else if (originalFileContent) {
+    // For JSON/JSONC files with existing content, use jsonc-parser to preserve comments
     try {
-      // Apply modifications to preserve existing structure
-      const editedContent = originalFileContent
-      const modifications: Array<jsonc.Edit> = []
-
-      // Generate edit operations for each key in the merged config
-      for (const key of Object.keys(mergedConfig)) {
-        const path = [key]
-        const edits = jsonc.modify(editedContent, path, mergedConfig[key], {
-          formattingOptions: { tabSize: 2, insertSpaces: true },
-        })
-        modifications.push(...edits)
-      }
-
-      // Apply all edits
-      configContent = jsonc.applyEdits(originalFileContent, modifications)
+      // Only modify the specific configKey path, preserving everything else
+      const configKeyPath = target.configKey.split('.')
+      const newValue = getNestedValue(mergedConfig, target.configKey)
+      const edits = jsonc.modify(originalFileContent, configKeyPath, newValue, {
+        formattingOptions: detectIndent(originalFileContent),
+      })
+      configContent = jsonc.applyEdits(originalFileContent, edits)
     } catch (error) {
       // Fallback to standard JSON.stringify if edit fails
       verbose(`Error applying JSONC edits: ${error instanceof Error ? error.message : String(error)}`)