import fs from 'fs';
import path from 'path';
import os from 'os';
import yaml from 'yaml';
import stripJsonComments from 'strip-json-comments';

const OPENCODE_CONFIG_DIR = path.join(os.homedir(), '.config', 'opencode');
const AGENT_DIR = path.join(OPENCODE_CONFIG_DIR, 'agent');
const COMMAND_DIR = path.join(OPENCODE_CONFIG_DIR, 'command');
const CONFIG_FILE = path.join(OPENCODE_CONFIG_DIR, 'opencode.json');
const CUSTOM_CONFIG_FILE = process.env.OPENCODE_CONFIG
  ? path.resolve(process.env.OPENCODE_CONFIG)
  : null;
const PROMPT_FILE_PATTERN = /^\{file:(.+)\}$/i;

// Scope types (shared by agents and commands)
const AGENT_SCOPE = {
  USER: 'user',
  PROJECT: 'project'
};

const COMMAND_SCOPE = {
  USER: 'user',
  PROJECT: 'project'
};

function ensureDirs() {
  if (!fs.existsSync(OPENCODE_CONFIG_DIR)) {
    fs.mkdirSync(OPENCODE_CONFIG_DIR, { recursive: true });
  }
  if (!fs.existsSync(AGENT_DIR)) {
    fs.mkdirSync(AGENT_DIR, { recursive: true });
  }
  if (!fs.existsSync(COMMAND_DIR)) {
    fs.mkdirSync(COMMAND_DIR, { recursive: true });
  }
}

// ============== AGENT SCOPE HELPERS ==============

/**
 * Ensure project-level agent directory exists
 */
function ensureProjectAgentDir(workingDirectory) {
  const projectAgentDir = path.join(workingDirectory, '.opencode', 'agent');
  if (!fs.existsSync(projectAgentDir)) {
    fs.mkdirSync(projectAgentDir, { recursive: true });
  }
  return projectAgentDir;
}

/**
 * Get project-level agent path
 */
function getProjectAgentPath(workingDirectory, agentName) {
  return path.join(workingDirectory, '.opencode', 'agent', `${agentName}.md`);
}

/**
 * Get user-level agent path
 */
function getUserAgentPath(agentName) {
  return path.join(AGENT_DIR, `${agentName}.md`);
}

/**
 * Determine agent scope based on where the .md file exists
 * Priority: project level > user level > null (built-in only)
 */
function getAgentScope(agentName, workingDirectory) {
  if (workingDirectory) {
    const projectPath = getProjectAgentPath(workingDirectory, agentName);
    if (fs.existsSync(projectPath)) {
      return { scope: AGENT_SCOPE.PROJECT, path: projectPath };
    }
  }
  
  const userPath = getUserAgentPath(agentName);
  if (fs.existsSync(userPath)) {
    return { scope: AGENT_SCOPE.USER, path: userPath };
  }
  
  return { scope: null, path: null };
}

/**
 * Get the path where an agent should be written based on scope
 */
function getAgentWritePath(agentName, workingDirectory, requestedScope) {
  // For updates: check existing location first (project takes precedence)
  const existing = getAgentScope(agentName, workingDirectory);
  if (existing.path) {
    return existing;
  }
  
  // For new agents or built-in overrides: use requested scope or default to user
  const scope = requestedScope || AGENT_SCOPE.USER;
  if (scope === AGENT_SCOPE.PROJECT && workingDirectory) {
    return { 
      scope: AGENT_SCOPE.PROJECT, 
      path: getProjectAgentPath(workingDirectory, agentName) 
    };
  }
  
  return { 
    scope: AGENT_SCOPE.USER, 
    path: getUserAgentPath(agentName) 
  };
}

// ============== COMMAND SCOPE HELPERS ==============

/**
 * Ensure project-level command directory exists
 */
function ensureProjectCommandDir(workingDirectory) {
  const projectCommandDir = path.join(workingDirectory, '.opencode', 'command');
  if (!fs.existsSync(projectCommandDir)) {
    fs.mkdirSync(projectCommandDir, { recursive: true });
  }
  return projectCommandDir;
}

/**
 * Get project-level command path
 */
function getProjectCommandPath(workingDirectory, commandName) {
  return path.join(workingDirectory, '.opencode', 'command', `${commandName}.md`);
}

/**
 * Get user-level command path
 */
function getUserCommandPath(commandName) {
  return path.join(COMMAND_DIR, `${commandName}.md`);
}

/**
 * Determine command scope based on where the .md file exists
 * Priority: project level > user level > null (built-in only)
 */
function getCommandScope(commandName, workingDirectory) {
  if (workingDirectory) {
    const projectPath = getProjectCommandPath(workingDirectory, commandName);
    if (fs.existsSync(projectPath)) {
      return { scope: COMMAND_SCOPE.PROJECT, path: projectPath };
    }
  }
  
  const userPath = getUserCommandPath(commandName);
  if (fs.existsSync(userPath)) {
    return { scope: COMMAND_SCOPE.USER, path: userPath };
  }
  
  return { scope: null, path: null };
}

/**
 * Get the path where a command should be written based on scope
 */
function getCommandWritePath(commandName, workingDirectory, requestedScope) {
  // For updates: check existing location first (project takes precedence)
  const existing = getCommandScope(commandName, workingDirectory);
  if (existing.path) {
    return existing;
  }
  
  // For new commands or built-in overrides: use requested scope or default to user
  const scope = requestedScope || COMMAND_SCOPE.USER;
  if (scope === COMMAND_SCOPE.PROJECT && workingDirectory) {
    return { 
      scope: COMMAND_SCOPE.PROJECT, 
      path: getProjectCommandPath(workingDirectory, commandName) 
    };
  }
  
  return { 
    scope: COMMAND_SCOPE.USER, 
    path: getUserCommandPath(commandName) 
  };
}

function isPromptFileReference(value) {
  if (typeof value !== 'string') {
    return false;
  }
  return PROMPT_FILE_PATTERN.test(value.trim());
}

function resolvePromptFilePath(reference) {
  const match = typeof reference === 'string' ? reference.trim().match(PROMPT_FILE_PATTERN) : null;
  if (!match) {
    return null;
  }
  let target = match[1].trim();
  if (!target) {
    return null;
  }

  if (target.startsWith('./')) {
    target = target.slice(2);
    target = path.join(OPENCODE_CONFIG_DIR, target);
  } else if (!path.isAbsolute(target)) {
    target = path.join(OPENCODE_CONFIG_DIR, target);
  }

  return target;
}

function writePromptFile(filePath, content) {
  const dir = path.dirname(filePath);
  fs.mkdirSync(dir, { recursive: true });
  fs.writeFileSync(filePath, content ?? '', 'utf8');
  console.log(`Updated prompt file: ${filePath}`);
}

function getProjectConfigPath(workingDirectory) {
  if (!workingDirectory) return null;
  return path.join(workingDirectory, 'opencode.json');
}

function getConfigPaths(workingDirectory) {
  return {
    userPath: CONFIG_FILE,
    projectPath: getProjectConfigPath(workingDirectory),
    customPath: CUSTOM_CONFIG_FILE
  };
}

function readConfigFile(filePath) {
  if (!filePath || !fs.existsSync(filePath)) {
    return {};
  }
  try {
    const content = fs.readFileSync(filePath, 'utf8');
    const normalized = stripJsonComments(content).trim();
    if (!normalized) {
      return {};
    }
    return JSON.parse(normalized);
  } catch (error) {
    console.error(`Failed to read config file: ${filePath}`, error);
    throw new Error('Failed to read OpenCode configuration');
  }
}

function isPlainObject(value) {
  return value && typeof value === 'object' && !Array.isArray(value);
}

function mergeConfigs(base, override) {
  if (!isPlainObject(base) || !isPlainObject(override)) {
    return override;
  }
  const result = { ...base };
  for (const [key, value] of Object.entries(override)) {
    if (key in result) {
      const baseValue = result[key];
      if (isPlainObject(baseValue) && isPlainObject(value)) {
        result[key] = mergeConfigs(baseValue, value);
      } else {
        result[key] = value;
      }
    } else {
      result[key] = value;
    }
  }
  return result;
}

function readConfigLayers(workingDirectory) {
  const { userPath, projectPath, customPath } = getConfigPaths(workingDirectory);
  const userConfig = readConfigFile(userPath);
  const projectConfig = readConfigFile(projectPath);
  const customConfig = readConfigFile(customPath);
  const mergedConfig = mergeConfigs(mergeConfigs(userConfig, projectConfig), customConfig);

  return {
    userConfig,
    projectConfig,
    customConfig,
    mergedConfig,
    paths: { userPath, projectPath, customPath }
  };
}

function readConfig(workingDirectory) {
  return readConfigLayers(workingDirectory).mergedConfig;
}

function writeConfig(config, filePath = CONFIG_FILE) {
  try {
    if (fs.existsSync(filePath)) {
      const backupFile = `${filePath}.openchamber.backup`;
      fs.copyFileSync(filePath, backupFile);
      console.log(`Created config backup: ${backupFile}`);
    }

    fs.mkdirSync(path.dirname(filePath), { recursive: true });
    fs.writeFileSync(filePath, JSON.stringify(config, null, 2), 'utf8');
    console.log(`Successfully wrote config file: ${filePath}`);
  } catch (error) {
    console.error(`Failed to write config file: ${filePath}`, error);
    throw new Error('Failed to write OpenCode configuration');
  }
}

function getJsonEntrySource(layers, sectionKey, entryName) {
  const { userConfig, projectConfig, customConfig, paths } = layers;
  const customSection = customConfig?.[sectionKey]?.[entryName];
  if (customSection !== undefined) {
    return { section: customSection, config: customConfig, path: paths.customPath, exists: true };
  }

  const projectSection = projectConfig?.[sectionKey]?.[entryName];
  if (projectSection !== undefined) {
    return { section: projectSection, config: projectConfig, path: paths.projectPath, exists: true };
  }

  const userSection = userConfig?.[sectionKey]?.[entryName];
  if (userSection !== undefined) {
    return { section: userSection, config: userConfig, path: paths.userPath, exists: true };
  }

  return { section: null, config: null, path: null, exists: false };
}

function getJsonWriteTarget(layers, preferredScope) {
  const { userConfig, projectConfig, customConfig, paths } = layers;
  if (paths.customPath) {
    return { config: customConfig, path: paths.customPath };
  }
  if (preferredScope === AGENT_SCOPE.PROJECT && paths.projectPath) {
    return { config: projectConfig, path: paths.projectPath };
  }
  if (paths.projectPath) {
    return { config: projectConfig, path: paths.projectPath };
  }
  return { config: userConfig, path: paths.userPath };
}

function parseMdFile(filePath) {
  try {
    const content = fs.readFileSync(filePath, 'utf8');
    const match = content.match(/^---\r?\n([\s\S]*?)\r?\n---\r?\n([\s\S]*)$/);

    if (!match) {
      return { frontmatter: {}, body: content.trim() };
    }

    const frontmatter = yaml.parse(match[1]) || {};
    const body = match[2].trim();

    return { frontmatter, body };
  } catch (error) {
    console.error(`Failed to parse markdown file ${filePath}:`, error);
    throw new Error('Failed to parse agent markdown file');
  }
}

function writeMdFile(filePath, frontmatter, body) {
  try {
    // Filter out null/undefined values - OpenCode expects keys to be omitted rather than set to null
    const cleanedFrontmatter = Object.fromEntries(
      Object.entries(frontmatter).filter(([, value]) => value != null)
    );
    const yamlStr = yaml.stringify(cleanedFrontmatter);
    const content = `---\n${yamlStr}---\n\n${body}`;
    fs.writeFileSync(filePath, content, 'utf8');
    console.log(`Successfully wrote markdown file: ${filePath}`);
  } catch (error) {
    console.error(`Failed to write markdown file ${filePath}:`, error);
    throw new Error('Failed to write agent markdown file');
  }
}

function getAgentSources(agentName, workingDirectory) {
  // Check project level first (takes precedence)
  const projectPath = workingDirectory ? getProjectAgentPath(workingDirectory, agentName) : null;
  const projectExists = projectPath && fs.existsSync(projectPath);
  
  // Then check user level
  const userPath = getUserAgentPath(agentName);
  const userExists = fs.existsSync(userPath);
  
  // Determine which md file to use (project takes precedence)
  const mdPath = projectExists ? projectPath : (userExists ? userPath : null);
  const mdExists = !!mdPath;
  const mdScope = projectExists ? AGENT_SCOPE.PROJECT : (userExists ? AGENT_SCOPE.USER : null);

  const layers = readConfigLayers(workingDirectory);
  const jsonSource = getJsonEntrySource(layers, 'agent', agentName);
  const jsonSection = jsonSource.section;
  const jsonPath = jsonSource.path || layers.paths.customPath || layers.paths.projectPath || layers.paths.userPath;
  const jsonScope = jsonSource.path === layers.paths.projectPath ? AGENT_SCOPE.PROJECT : AGENT_SCOPE.USER;

  const sources = {
    md: {
      exists: mdExists,
      path: mdPath,
      scope: mdScope,
      fields: []
    },
    json: {
      exists: jsonSource.exists,
      path: jsonPath,
      scope: jsonSource.exists ? jsonScope : null,
      fields: []
    },
    json: {
      exists: jsonSource.exists,
      path: jsonPath,
      scope: jsonSource.exists ? jsonScope : null,
      fields: []
    },
    // Additional info about both levels
    projectMd: {
      exists: projectExists,
      path: projectPath
    },
    userMd: {
      exists: userExists,
      path: userPath
    }
  };

  if (mdExists) {
    const { frontmatter, body } = parseMdFile(mdPath);
    sources.md.fields = Object.keys(frontmatter);
    if (body) {
      sources.md.fields.push('prompt');
    }
  }

  if (jsonSection) {
    sources.json.fields = Object.keys(jsonSection);
  }

  return sources;
}

function createAgent(agentName, config, workingDirectory, scope) {
  ensureDirs();

  // Check if agent already exists at either level
  const projectPath = workingDirectory ? getProjectAgentPath(workingDirectory, agentName) : null;
  const userPath = getUserAgentPath(agentName);
  
  if (projectPath && fs.existsSync(projectPath)) {
    throw new Error(`Agent ${agentName} already exists as project-level .md file`);
  }
  
  if (fs.existsSync(userPath)) {
    throw new Error(`Agent ${agentName} already exists as user-level .md file`);
  }

  const layers = readConfigLayers(workingDirectory);
  const jsonSource = getJsonEntrySource(layers, 'agent', agentName);
  if (jsonSource.exists) {
    throw new Error(`Agent ${agentName} already exists in opencode.json`);
  }

  // Determine target path based on requested scope
  let targetPath;
  let targetScope;
  
  if (scope === AGENT_SCOPE.PROJECT && workingDirectory) {
    ensureProjectAgentDir(workingDirectory);
    targetPath = projectPath;
    targetScope = AGENT_SCOPE.PROJECT;
  } else {
    targetPath = userPath;
    targetScope = AGENT_SCOPE.USER;
  }

  // Extract scope and prompt from config - scope is only used for path determination, not written to file
  const { prompt, scope: _scopeFromConfig, ...frontmatter } = config;

  writeMdFile(targetPath, frontmatter, prompt || '');
  console.log(`Created new agent: ${agentName} (scope: ${targetScope}, path: ${targetPath})`);
}

function updateAgent(agentName, updates, workingDirectory) {
  ensureDirs();

  // Determine correct path: project level takes precedence
  const { scope, path: mdPath } = getAgentWritePath(agentName, workingDirectory);
  const mdExists = mdPath && fs.existsSync(mdPath);
  
  // Check if agent exists in opencode.json across all config layers
  const layers = readConfigLayers(workingDirectory);
  const jsonSource = getJsonEntrySource(layers, 'agent', agentName);
  const jsonSection = jsonSource.section;
  const hasJsonFields = jsonSource.exists && jsonSection && Object.keys(jsonSection).length > 0;
  const jsonTarget = jsonSource.exists
    ? { config: jsonSource.config, path: jsonSource.path }
    : getJsonWriteTarget(layers, workingDirectory ? AGENT_SCOPE.PROJECT : AGENT_SCOPE.USER);
  let config = jsonTarget.config || {};
  
  // Determine if we should create a new md file:
  // Only for built-in agents (no md file AND no json config)
  const isBuiltinOverride = !mdExists && !hasJsonFields;
  
  let targetPath = mdPath;
  let targetScope = scope;
  
  if (!mdExists && isBuiltinOverride) {
    // Built-in agent override - create at user level
    targetPath = getUserAgentPath(agentName);
    targetScope = AGENT_SCOPE.USER;
  }

  // Only create md data for existing md files or built-in overrides
  let mdData = mdExists ? parseMdFile(mdPath) : (isBuiltinOverride ? { frontmatter: {}, body: '' } : null);

  let mdModified = false;
  let jsonModified = false;
  // Only create new md if it's a built-in override
  let creatingNewMd = isBuiltinOverride;

  for (const [field, value] of Object.entries(updates)) {

    if (field === 'prompt') {
      const normalizedValue = typeof value === 'string' ? value : (value == null ? '' : String(value));

      if (mdExists || creatingNewMd) {
        if (mdData) {
          mdData.body = normalizedValue;
          mdModified = true;
        }
        continue;
      } else if (isPromptFileReference(jsonSection?.prompt)) {
        const promptFilePath = resolvePromptFilePath(jsonSection.prompt);
        if (!promptFilePath) {
          throw new Error(`Invalid prompt file reference for agent ${agentName}`);
        }
        writePromptFile(promptFilePath, normalizedValue);
        continue;
      } else if (isPromptFileReference(normalizedValue)) {
        if (!config.agent) config.agent = {};
        if (!config.agent[agentName]) config.agent[agentName] = {};
        config.agent[agentName].prompt = normalizedValue;
        jsonModified = true;
        continue;
      }
      
      // For JSON-only agents, store prompt inline in JSON
      if (!config.agent) config.agent = {};
      if (!config.agent[agentName]) config.agent[agentName] = {};
      config.agent[agentName].prompt = normalizedValue;
      jsonModified = true;
      continue;
    }

    const inMd = mdData?.frontmatter?.[field] !== undefined;
    const inJson = jsonSection?.[field] !== undefined;

    // JSON takes precedence over md, so update JSON first if field exists there
    if (inJson) {
      if (!config.agent) config.agent = {};
      if (!config.agent[agentName]) config.agent[agentName] = {};
      config.agent[agentName][field] = value;
      jsonModified = true;
    } else if (inMd || creatingNewMd) {
      if (mdData) {
        mdData.frontmatter[field] = value;
        mdModified = true;
      }
    } else {
      // New field - add to the appropriate location based on agent source
      if ((mdExists || creatingNewMd) && mdData) {
        mdData.frontmatter[field] = value;
        mdModified = true;
      } else {
        // JSON-only agent or has JSON fields - add to JSON
        if (!config.agent) config.agent = {};
        if (!config.agent[agentName]) config.agent[agentName] = {};
        config.agent[agentName][field] = value;
        jsonModified = true;
      }
    }
  }

  if (mdModified && mdData) {
    writeMdFile(targetPath, mdData.frontmatter, mdData.body);
  }

  if (jsonModified) {
    writeConfig(config, jsonTarget.path || CONFIG_FILE);
  }

  console.log(`Updated agent: ${agentName} (scope: ${targetScope}, md: ${mdModified}, json: ${jsonModified})`);
}

function deleteAgent(agentName, workingDirectory) {
  let deleted = false;

  // Check project level first (takes precedence)
  if (workingDirectory) {
    const projectPath = getProjectAgentPath(workingDirectory, agentName);
    if (fs.existsSync(projectPath)) {
      fs.unlinkSync(projectPath);
      console.log(`Deleted project-level agent .md file: ${projectPath}`);
      deleted = true;
    }
  }

  // Then check user level
  const userPath = getUserAgentPath(agentName);
  if (fs.existsSync(userPath)) {
    fs.unlinkSync(userPath);
    console.log(`Deleted user-level agent .md file: ${userPath}`);
    deleted = true;
  }

  // Also check json config (highest precedence entry only)
  const layers = readConfigLayers(workingDirectory);
  const jsonSource = getJsonEntrySource(layers, 'agent', agentName);
  if (jsonSource.exists && jsonSource.config && jsonSource.path) {
    if (!jsonSource.config.agent) jsonSource.config.agent = {};
    delete jsonSource.config.agent[agentName];
    writeConfig(jsonSource.config, jsonSource.path);
    console.log(`Removed agent from opencode.json: ${agentName}`);
    deleted = true;
  }

  // If nothing was deleted (built-in agent), disable it in highest-precedence config
  if (!deleted) {
    const jsonTarget = getJsonWriteTarget(layers, workingDirectory ? AGENT_SCOPE.PROJECT : AGENT_SCOPE.USER);
    const targetConfig = jsonTarget.config || {};
    if (!targetConfig.agent) targetConfig.agent = {};
    targetConfig.agent[agentName] = { disable: true };
    writeConfig(targetConfig, jsonTarget.path || CONFIG_FILE);
    console.log(`Disabled built-in agent: ${agentName}`);
  }
}

function getCommandSources(commandName, workingDirectory) {
  // Check project level first (takes precedence)
  const projectPath = workingDirectory ? getProjectCommandPath(workingDirectory, commandName) : null;
  const projectExists = projectPath && fs.existsSync(projectPath);
  
  // Then check user level
  const userPath = getUserCommandPath(commandName);
  const userExists = fs.existsSync(userPath);
  
  // Determine which md file to use (project takes precedence)
  const mdPath = projectExists ? projectPath : (userExists ? userPath : null);
  const mdExists = !!mdPath;
  const mdScope = projectExists ? COMMAND_SCOPE.PROJECT : (userExists ? COMMAND_SCOPE.USER : null);

  const layers = readConfigLayers(workingDirectory);
  const jsonSource = getJsonEntrySource(layers, 'command', commandName);
  const jsonSection = jsonSource.section;
  const jsonPath = jsonSource.path || layers.paths.customPath || layers.paths.projectPath || layers.paths.userPath;

  const sources = {
    md: {
      exists: mdExists,
      path: mdPath,
      scope: mdScope,
      fields: []
    },
    json: {
      exists: jsonSource.exists,
      path: jsonPath,
      fields: []
    },
    // Additional info about both levels
    projectMd: {
      exists: projectExists,
      path: projectPath
    },
    userMd: {
      exists: userExists,
      path: userPath
    }
  };

  if (mdExists) {
    const { frontmatter, body } = parseMdFile(mdPath);
    sources.md.fields = Object.keys(frontmatter);
    if (body) {
      sources.md.fields.push('template');
    }
  }

  if (jsonSection) {
    sources.json.fields = Object.keys(jsonSection);
  }

  return sources;
}

function createCommand(commandName, config, workingDirectory, scope) {
  ensureDirs();

  // Check if command already exists at either level
  const projectPath = workingDirectory ? getProjectCommandPath(workingDirectory, commandName) : null;
  const userPath = getUserCommandPath(commandName);
  
  if (projectPath && fs.existsSync(projectPath)) {
    throw new Error(`Command ${commandName} already exists as project-level .md file`);
  }
  
  if (fs.existsSync(userPath)) {
    throw new Error(`Command ${commandName} already exists as user-level .md file`);
  }

  const layers = readConfigLayers(workingDirectory);
  const jsonSource = getJsonEntrySource(layers, 'command', commandName);
  if (jsonSource.exists) {
    throw new Error(`Command ${commandName} already exists in opencode.json`);
  }

  // Determine target path based on requested scope
  let targetPath;
  let targetScope;
  
  if (scope === COMMAND_SCOPE.PROJECT && workingDirectory) {
    ensureProjectCommandDir(workingDirectory);
    targetPath = projectPath;
    targetScope = COMMAND_SCOPE.PROJECT;
  } else {
    targetPath = userPath;
    targetScope = COMMAND_SCOPE.USER;
  }

  // Extract scope from config - it's only used for path determination, not written to file
  const { template, scope: _scopeFromConfig, ...frontmatter } = config;

  writeMdFile(targetPath, frontmatter, template || '');
  console.log(`Created new command: ${commandName} (scope: ${targetScope}, path: ${targetPath})`);
}

function updateCommand(commandName, updates, workingDirectory) {
  ensureDirs();

  // Determine correct path: project level takes precedence
  const { scope, path: mdPath } = getCommandWritePath(commandName, workingDirectory);
  const mdExists = mdPath && fs.existsSync(mdPath);

  const layers = readConfigLayers(workingDirectory);
  const jsonSource = getJsonEntrySource(layers, 'command', commandName);
  const jsonSection = jsonSource.section;
  const hasJsonFields = jsonSource.exists && jsonSection && Object.keys(jsonSection).length > 0;
  const jsonTarget = jsonSource.exists
    ? { config: jsonSource.config, path: jsonSource.path }
    : getJsonWriteTarget(layers, workingDirectory ? COMMAND_SCOPE.PROJECT : COMMAND_SCOPE.USER);
  let config = jsonTarget.config || {};

  // Only create a new md file for built-in overrides (no md + no json)
  const isBuiltinOverride = !mdExists && !hasJsonFields;

  let targetPath = mdPath;
  let targetScope = scope;

  if (!mdExists && isBuiltinOverride) {
    // Built-in command override - create at user level
    targetPath = getUserCommandPath(commandName);
    targetScope = COMMAND_SCOPE.USER;
  }

  const mdData = mdExists ? parseMdFile(mdPath) : (isBuiltinOverride ? { frontmatter: {}, body: '' } : null);

  let mdModified = false;
  let jsonModified = false;
  let creatingNewMd = isBuiltinOverride;

  for (const [field, value] of Object.entries(updates)) {

    if (field === 'template') {
      const normalizedValue = typeof value === 'string' ? value : (value == null ? '' : String(value));

      if (mdExists || creatingNewMd) {
        if (mdData) {
          mdData.body = normalizedValue;
          mdModified = true;
        }
        continue;
      } else if (isPromptFileReference(jsonSection?.template)) {
        const templateFilePath = resolvePromptFilePath(jsonSection.template);
        if (!templateFilePath) {
          throw new Error(`Invalid template file reference for command ${commandName}`);
        }
        writePromptFile(templateFilePath, normalizedValue);
        continue;
      } else if (isPromptFileReference(normalizedValue)) {
        if (!config.command) config.command = {};
        if (!config.command[commandName]) config.command[commandName] = {};
        config.command[commandName].template = normalizedValue;
        jsonModified = true;
        continue;
      }

      // For JSON-only commands, store template inline in JSON
      if (!config.command) config.command = {};
      if (!config.command[commandName]) config.command[commandName] = {};
      config.command[commandName].template = normalizedValue;
      jsonModified = true;
      continue;
    }

    const inMd = mdData?.frontmatter?.[field] !== undefined;
    const inJson = jsonSection?.[field] !== undefined;

    // JSON takes precedence over md, so update JSON first if field exists there
    if (inJson) {
      if (!config.command) config.command = {};
      if (!config.command[commandName]) config.command[commandName] = {};
      config.command[commandName][field] = value;
      jsonModified = true;
    } else if (inMd || creatingNewMd) {
      if (mdData) {
        mdData.frontmatter[field] = value;
        mdModified = true;
      }
    } else {
      // New field - add to appropriate location based on command source
      if ((mdExists || creatingNewMd) && mdData) {
        mdData.frontmatter[field] = value;
        mdModified = true;
      } else {
        if (!config.command) config.command = {};
        if (!config.command[commandName]) config.command[commandName] = {};
        config.command[commandName][field] = value;
        jsonModified = true;
      }
    }
  }

  if (mdModified && mdData) {
    writeMdFile(targetPath, mdData.frontmatter, mdData.body);
  }

  if (jsonModified) {
    writeConfig(config, jsonTarget.path || CONFIG_FILE);
  }

  console.log(`Updated command: ${commandName} (scope: ${targetScope}, md: ${mdModified}, json: ${jsonModified})`);
}

function deleteCommand(commandName, workingDirectory) {
  let deleted = false;

  // Check project level first (takes precedence)
  if (workingDirectory) {
    const projectPath = getProjectCommandPath(workingDirectory, commandName);
    if (fs.existsSync(projectPath)) {
      fs.unlinkSync(projectPath);
      console.log(`Deleted project-level command .md file: ${projectPath}`);
      deleted = true;
    }
  }

  // Then check user level
  const userPath = getUserCommandPath(commandName);
  if (fs.existsSync(userPath)) {
    fs.unlinkSync(userPath);
    console.log(`Deleted user-level command .md file: ${userPath}`);
    deleted = true;
  }

  // Also check json config (highest precedence entry only)
  const layers = readConfigLayers(workingDirectory);
  const jsonSource = getJsonEntrySource(layers, 'command', commandName);
  if (jsonSource.exists && jsonSource.config && jsonSource.path) {
    if (!jsonSource.config.command) jsonSource.config.command = {};
    delete jsonSource.config.command[commandName];
    writeConfig(jsonSource.config, jsonSource.path);
    console.log(`Removed command from opencode.json: ${commandName}`);
    deleted = true;
  }

  if (!deleted) {
    throw new Error(`Command "${commandName}" not found`);
  }
}

export {
  getAgentSources,
  getAgentScope,
  createAgent,
  updateAgent,
  deleteAgent,
  getCommandSources,
  getCommandScope,
  createCommand,
  updateCommand,
  deleteCommand,
  readConfig,
  writeConfig,
  AGENT_DIR,
  COMMAND_DIR,
  CONFIG_FILE,
  AGENT_SCOPE,
  COMMAND_SCOPE
};