feat: add TypeDoc @group annotations and configuration enhancements

- Update typedoc.markdown.json with multiple entry points and categorization
- Add @group annotations to core API functions in src/index.ts
- Add @group annotations to command functions in src/commands/
- Enable excludeNotDocumented and categorizeByGroup options
- Improve JSDoc documentation with bash examples
- Configure category ordering for better documentation structure

Author: Mearman

src/commands/convert.ts

@@ -50,7 +50,7 @@ export interface ConvertOptions {
  *
  *   // Recursive directory processing
  *   await expandSourcePatterns(['docs/'], { recursive: true });
- *   ```;
+ *   ```
  *
  * @param patterns - Array of file patterns, paths, or directories to expand
  * @param options - Conversion options including recursive processing
@@ -224,7 +224,7 @@ function printConvertSummary(
  * Processes markdown files to convert link formats and path resolution according to specified
  * options. Supports dry run mode, verbose output, and various conversion strategies.
  *
- * @category Commands
+ * @group Commands
  *
  * @example
  *   ```bash
@@ -236,7 +236,7 @@ function printConvertSummary(
  *
  *   # Dry run with verbose output
  *   markmv convert README.md --link-style claude --dry-run --verbose
- *   ```;
+ *   ```
  *
  * @param patterns - File patterns to process (supports globs)
  * @param options - Command options specifying conversion parameters

src/commands/index.ts

@@ -104,6 +104,29 @@ interface IndexCliOptions {
   boundary?: string;
 }
 
+/**
+ * CLI command handler for generating documentation indexes.
+ *
+ * Creates organized documentation indexes from markdown files using various strategies.
+ * Supports multiple index types including links, imports, embeds, and hybrid modes.
+ *
+ * @group Commands
+ *
+ * @example
+ *   ```bash
+ *   # Generate a links-based index
+ *   markmv index --type links --strategy directory
+ *
+ *   # Generate with custom template
+ *   markmv index docs/ --type hybrid --template custom.md
+ *
+ *   # Dry run with verbose output
+ *   markmv index --dry-run --verbose
+ *   ```
+ *
+ * @param directory - Target directory for index generation
+ * @param cliOptions - Command options specifying index parameters
+ */
 export async function indexCommand(
   directory: string | undefined,
   cliOptions: IndexCliOptions

src/index.ts

@@ -130,13 +130,15 @@ export type {
  * Creates a new FileOperations instance for performing markdown file operations. This is the
  * recommended way to get started with the library.
  *
+ * @group Core API
+ *
  * @example
  *   ```typescript
  *   import { createMarkMv } from 'markmv';
  *
  *   const markmv = createMarkMv();
  *   const result = await markmv.moveFile('old.md', 'new.md');
- *   ```;
+ *   ```
  *
  * @returns A new FileOperations instance
  */
@@ -147,14 +149,16 @@ export function createMarkMv(): FileOperations {
 /**
  * Convenience function for moving a single markdown file
  *
+ * @group Core API
+ *
  * @example
  *   ```typescript
  *   import { moveFile } from 'markmv';
  *
  *   const result = await moveFile('docs/old.md', 'docs/new.md', {
  *     dryRun: true
  *   });
- *   ```;
+ *   ```
  *
  * @param sourcePath - The current file path
  * @param destinationPath - The target file path
@@ -174,6 +178,8 @@ export async function moveFile(
 /**
  * Convenience function for moving multiple markdown files
  *
+ * @group Core API
+ *
  * @example
  *   ```typescript
  *   import { moveFiles } from 'markmv';
@@ -182,7 +188,7 @@ export async function moveFile(
  *     { source: 'old1.md', destination: 'new1.md' },
  *     { source: 'old2.md', destination: 'new2.md' }
  *   ]);
- *   ```;
+ *   ```
  *
  * @param moves - Array of source/destination pairs
  * @param options - Optional configuration
@@ -200,6 +206,8 @@ export async function moveFiles(
 /**
  * Convenience function for validating markdown file operations
  *
+ * @group Core API
+ *
  * @example
  *   ```typescript
  *   import { moveFile, validateOperation } from 'markmv';

typedoc.markdown.json

@@ -1,21 +1,22 @@
 {
   "$schema": "https://typedoc.org/schema.json",
   "plugin": ["typedoc-plugin-markdown"],
-  "entryPoints": ["src/index.ts"],
+  "entryPoints": ["src/index.ts", "src/commands/convert.ts", "src/commands/index.ts"],
   "out": "docs-markdown",
   "name": "markmv",
   "includeVersion": true,
   "excludePrivate": true,
   "excludeProtected": false,
   "excludeInternal": false,
-  "readme": "none",
+  "excludeNotDocumented": true,
+  "readme": "templates/README-for-typedoc.md",
   "gitRevision": "main",
   "gitRemote": "origin",
   "sourceLinkTemplate": "https://github.com/ExaDev/markmv/blob/{gitRevision}/{path}#L{line}",
   "categorizeByGroup": true,
   "defaultCategory": "Other",
   "categoryOrder": [
-    "Core",
+    "Core API",
     "Commands", 
     "Strategies",
     "Types",
@@ -34,16 +35,22 @@
     "**/*.test.ts",
     "**/*.spec.ts",
     "**/cli.ts",
+    "**/mcp-server.ts",
+    "**/api-server.ts",
     "node_modules/**/*"
   ],
   "externalPattern": [
     "**/node_modules/**"
   ],
-  "outputFileStrategy": "members",
-  "mergeReadme": false,
-  "hidePageHeader": false,
+  "outputFileStrategy": "modules",
+  "mergeReadme": true,
+  "hidePageHeader": true,
   "hideBreadcrumbs": true,
-  "hidePageTitle": false,
+  "hidePageTitle": true,
+  "useCodeBlocks": true,
+  "expandParameters": true,
+  "outputFileStrategy": "modules",
+  "flattenOutputFiles": true,
   "titleLink": "https://github.com/ExaDev/markmv",
   "navigationLinks": {
     "GitHub": "https://github.com/ExaDev/markmv",