diff --git a/packages/typedoc-plugin-markdown/src/index.ts b/packages/typedoc-plugin-markdown/src/index.ts
index 5fbd1e81a..8ffc73d5e 100644
--- a/packages/typedoc-plugin-markdown/src/index.ts
+++ b/packages/typedoc-plugin-markdown/src/index.ts
@@ -1,11 +1,16 @@
-import * as fs from 'fs';
 import * as path from 'path';
 
-import { Application, Converter, ParameterType, Renderer } from 'typedoc';
+import { Application, ParameterType } from 'typedoc';
 
+import { CustomOptionsReader } from './options-reader';
 import MarkdownTheme from './theme';
 
 export function load(app: Application) {
+  addDeclarations(app);
+  loadTheme(app);
+}
+
+function addDeclarations(app: Application) {
   app.options.addDeclaration({
     help: '[Markdown Plugin] Do not render page title.',
     name: 'hidePageTitle',
@@ -21,23 +26,20 @@ export function load(app: Application) {
   });
 
   app.options.addDeclaration({
-    help:
-      '[Markdown Plugin] Specifies the base path that all links to be served from. If omitted all urls will be relative.',
+    help: '[Markdown Plugin] Specifies the base path that all links to be served from. If omitted all urls will be relative.',
     name: 'publicPath',
     type: ParameterType.String,
   });
 
   app.options.addDeclaration({
-    help:
-      '[Markdown Plugin] Use HTML named anchors as fragment identifiers for engines that do not automatically assign header ids. Should be set for Bitbucket Server docs.',
+    help: '[Markdown Plugin] Use HTML named anchors as fragment identifiers for engines that do not automatically assign header ids. Should be set for Bitbucket Server docs.',
     name: 'namedAnchors',
     type: ParameterType.Boolean,
     defaultValue: false,
   });
 
   app.options.addDeclaration({
-    help:
-      '[Markdown Plugin] Output all reflections into seperate output files.',
+    help: '[Markdown Plugin] Output all reflections into seperate output files.',
     name: 'allReflectionsHaveOwnDocument',
     type: ParameterType.Boolean,
     defaultValue: false,
@@ -69,37 +71,35 @@ export function load(app: Application) {
     name: 'indexTitle',
     type: ParameterType.String,
   });
+}
 
-  app.converter.on(Converter.EVENT_BEGIN, () => {
-    Renderer.getDefaultTheme = () => path.join(__dirname, 'resources');
-  });
-
-  app.converter.on(Converter.EVENT_RESOLVE_BEGIN, () => {
-    const themeName = app.options.getValue('theme');
-
-    const themeDir = path.join(__dirname);
-
-    if (![themeDir, 'default', 'markdown'].includes(themeName)) {
-      // For custom themes check that the theme is a markdown theme
-      // If it is return and pass through to renderer
-      const themeFileName = path.resolve(path.join(themeName, 'theme.js'));
-      if (fs.existsSync(themeFileName) && isMarkdownTheme(themeFileName)) {
-        return;
-      }
+function loadTheme(app: Application) {
+  const themeRef = app.options.getValue('theme');
+  const themeDir = path.join(__dirname);
+  const basePath = themeDir + '/resources';
+
+  if ([themeDir, 'default', 'markdown'].includes(themeRef)) {
+    app.renderer.theme = new MarkdownTheme(app.renderer, basePath);
+  } else {
+    const CustomTheme = getCustomTheme(
+      path.resolve(path.join(themeRef, 'theme.js')),
+    );
+    if (CustomTheme !== null) {
+      app.options.addReader(new CustomOptionsReader());
+      app.renderer.theme = new CustomTheme(app.renderer, basePath);
+    } else {
       app.logger.warn(
-        `[typedoc-plugin-markdown] '${themeName}' is not a recognised markdown theme. If an html theme is required, please disable this plugin.`,
+        `[typedoc-plugin-markdown] '${themeRef}' is not a recognised markdown theme.`,
       );
     }
-
-    app.options.setValue('theme', themeDir);
-  });
+  }
 }
 
-function isMarkdownTheme(themeFileName: string) {
+function getCustomTheme(themeFile: string) {
   try {
-    const ThemeClass = require(themeFileName).default;
-    return ThemeClass.prototype instanceof MarkdownTheme;
+    const ThemeClass = require(themeFile).default;
+    return ThemeClass.prototype instanceof MarkdownTheme ? ThemeClass : null;
   } catch (e) {
-    return false;
+    return null;
   }
 }
diff --git a/packages/typedoc-plugin-markdown/src/options-reader.ts b/packages/typedoc-plugin-markdown/src/options-reader.ts
new file mode 100644
index 000000000..22a3349e1
--- /dev/null
+++ b/packages/typedoc-plugin-markdown/src/options-reader.ts
@@ -0,0 +1,29 @@
+import * as path from 'path';
+
+import { Options, OptionsReader } from 'typedoc';
+import { Logger } from 'typedoc/dist/lib/utils';
+
+export class CustomOptionsReader implements OptionsReader {
+  priority = 900;
+
+  name = 'custom-options';
+
+  read(container: Options, logger: Logger) {
+    const options = this.getOptionsFile(
+      path.resolve(path.join(container.getValue('theme'), 'options.js')),
+    );
+    if (options) {
+      Object.entries(options).forEach(([key, value]) => {
+        container.setValue(key, value);
+      });
+    }
+  }
+
+  getOptionsFile(optionsFile: string) {
+    try {
+      return require(optionsFile).default;
+    } catch (e) {
+      return null;
+    }
+  }
+}
diff --git a/packages/typedoc-plugin-markdown/src/theme.ts b/packages/typedoc-plugin-markdown/src/theme.ts
index cc585f08b..af998fff3 100644
--- a/packages/typedoc-plugin-markdown/src/theme.ts
+++ b/packages/typedoc-plugin-markdown/src/theme.ts
@@ -38,7 +38,7 @@ export default class MarkdownTheme extends Theme {
   @BindOption('filenameSeparator')
   filenameSeparator!: string;
   @BindOption('entryDocument')
-  entryDocument!: string;
+  entryDocument: string;
 
   // creates an isolated Handlebars environment to store context aware helpers
   static HANDLEBARS = Handlebars.create();
@@ -237,12 +237,8 @@ export default class MarkdownTheme extends Theme {
       const navigationItem = new NavigationItem(title, url);
       navigationItem.isLabel = isLabel;
       navigationItem.children = children;
-      const {
-        reflection,
-        parent,
-        cssClasses,
-        ...filteredNavigationItem
-      } = navigationItem;
+      const { reflection, parent, cssClasses, ...filteredNavigationItem } =
+        navigationItem;
       return filteredNavigationItem as NavigationItem;
     };
     const navigation = createNavigationItem(project.name, undefined, false);
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/comments.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/comments.spec.ts.snap
index f39e617dd..22bf6863d 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/comments.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/comments.spec.ts.snap
@@ -11,7 +11,7 @@ You can write <strong>HTML</strong> tags directly in comments
 `;
 
 exports[`Comments: should build @link references' 1`] = `
-"See [\`CommentClass\`](commentclass.md) and [CommentClass's comment property](commentclass.md#comment).
+"See [\`CommentClass\`](CommentClass.md) and [CommentClass's comment property](CommentClass.md#comment).
 Also, check out [Google](https://www.google.com) and
 [GitHub](https://github.com).
 
@@ -61,7 +61,7 @@ Another tag description
 exports[`Comments: should convert symbols brackets to symbol links' 1`] = `
 "Additionally you can link to other classes, members or functions using double square brackets.
 
-- Link to an external reflection: [CommentClass](commentclass.md)
+- Link to an external reflection: [CommentClass](CommentClass.md)
 - Link to an internal reflection: [commentsInReturn](../modules.md#commentsinreturn)
 - Link to an undefined reflection: [[VOID]]
 "
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/generics.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/generics.spec.ts.snap
index 4d593cd30..9df046031 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/generics.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/generics.spec.ts.snap
@@ -46,7 +46,7 @@ exports[`Generics: should compile function with complex type params' 1`] = `
 
 | Name | Type | Description |
 | :------ | :------ | :------ |
-| \`A\` | extends [\`ClassWithTypeParams\`](classwithtypeparams.md)<\`string\`, \`number\`, \`A\`\\\\> | Comment for type \`A\` |
+| \`A\` | extends [\`ClassWithTypeParams\`](ClassWithTypeParams.md)<\`string\`, \`number\`, \`A\`\\\\> | Comment for type \`A\` |
 | \`B\` | \`string\` \\\\| \`boolean\` | Comment for type \`B\` |
 | \`C\` | \`string\` | - |
 
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/hierarchy.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/hierarchy.spec.ts.snap
index f42e153c7..94a58ec06 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/hierarchy.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/hierarchy.spec.ts.snap
@@ -1,19 +1,19 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`Hierarchy: should compile nested type hierarchy 1`] = `
-"- [\`ParentClass\`](parentclass.md)
+"- [\`ParentClass\`](ParentClass.md)
 
   ↳ **\`ChildClassA\`**
 
-  ↳↳ [\`GrandChildClassA\`](grandchildclassa.md)
+  ↳↳ [\`GrandChildClassA\`](GrandChildClassA.md)
 "
 `;
 
 exports[`Hierarchy: should compile type hierarchy 1`] = `
 "- **\`ParentClass\`**
 
-  ↳ [\`ChildClassA\`](childclassa.md)
+  ↳ [\`ChildClassA\`](ChildClassA.md)
 
-  ↳ [\`ChildClassB\`](childclassb.md)
+  ↳ [\`ChildClassB\`](ChildClassB.md)
 "
 `;
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/options.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/options.spec.ts.snap
index ff3fe1ef5..8357a8118 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/options.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/options.spec.ts.snap
@@ -1,5 +1,5 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`Options: (defaults) should compile relativeURL helper 1`] = `"breadcrumbs.md"`;
+exports[`Options: (defaults) should compile relativeURL helper 1`] = `"Breadcrumbs.md"`;
 
-exports[`Options: (with plugin options) should compile relativeURL helper with public path 1`] = `"test-public-pathclasses/breadcrumbs.md"`;
+exports[`Options: (with plugin options) should compile relativeURL helper with public path 1`] = `"test-public-pathclasses/Breadcrumbs.md"`;
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/reflections.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/reflections.spec.ts.snap
index d566db6d9..af06245a8 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/reflections.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/reflections.spec.ts.snap
@@ -12,7 +12,14 @@ exports[`Reflections: (header) should compile template with breadcrumbs and with
 exports[`Reflections: (template) should compile Enum 1`] = `
 "# Enumeration: EnumReflection
 
-[helper: toc]
+## Table of contents
+
+### Enumeration members
+
+- [Down](../enums/EnumReflection.md#down)
+- [Left](../enums/EnumReflection.md#left)
+- [Right](../enums/EnumReflection.md#right)
+- [Up](../enums/EnumReflection.md#up)
 
 [partial: members]
 "
@@ -27,8 +34,6 @@ exports[`Reflections: (template) should compile a callable reflection 1`] = `
 
 [partial: member.signature]
 
-[helper: toc]
-
 [partial: members]
 "
 `;
@@ -42,8 +47,6 @@ exports[`Reflections: (template) should compile an indexable reflection 1`] = `
 
 [partial: comment]
 
-[helper: toc]
-
 [partial: members]
 "
 `;
@@ -53,9 +56,13 @@ exports[`Reflections: (template) should compile implemented class 1`] = `
 
 ## Implements
 
-- [\`ReflectionClass\`](../classes/reflectionclass.md)
+- [\`ReflectionClass\`](../classes/ReflectionClass.md)
 
-[helper: toc]
+## Table of contents
+
+### Constructors
+
+- [constructor](../classes/ImplementedClass.md#constructor)
 
 [partial: members]
 "
@@ -64,7 +71,14 @@ exports[`Reflections: (template) should compile implemented class 1`] = `
 exports[`Reflections: (template) should compile module with breadcrumbs and project title 1`] = `
 "# Enumeration: EnumReflection
 
-[helper: toc]
+## Table of contents
+
+### Enumeration members
+
+- [Down](../enums/EnumReflection.md#down)
+- [Left](../enums/EnumReflection.md#left)
+- [Right](../enums/EnumReflection.md#right)
+- [Up](../enums/EnumReflection.md#up)
 
 [partial: members]
 "
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/signatures.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/signatures.spec.ts.snap
index 254970184..fe90bf38f 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/signatures.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/signatures.spec.ts.snap
@@ -84,7 +84,7 @@ Some nested params.
 | \`params.nestedObj\` | \`Object\` | A nested object. |
 | \`params.nestedObj.name\` | \`string\` | - |
 | \`params.nestedObj.obj\` | \`Object\` | - |
-| \`params.nestedObj.obj.name\` | () => \`void\` | - |
+| \`params.nestedObj.obj.name\` |  | - |
 | \`params.nestedObj.value\` | \`number\` | - |
 | \`params.parent?\` | \`number\` | - |
 | \`context\` | \`any\` | The context of the method call. |
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/sources.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/sources.spec.ts.snap
index e08f307a9..64c5e57a2 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/sources.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/sources.spec.ts.snap
@@ -3,7 +3,7 @@
 exports[`Sources: should display implementation of sources' 1`] = `
 "#### Implementation of
 
-[SomeInterface](someinterface.md).[prop](someinterface.md#prop)
+[SomeInterface](SomeInterface.md).[prop](SomeInterface.md#prop)
 
 #### Defined in
 
@@ -14,7 +14,7 @@ sources.ts:6
 exports[`Sources: should display inherited sources' 1`] = `
 "#### Inherited from
 
-[SomeClass](../classes/someclass.md).[prop](../classes/someclass.md#prop)
+[SomeClass](../classes/SomeClass.md).[prop](../classes/SomeClass.md#prop)
 
 #### Defined in
 
@@ -25,7 +25,7 @@ sources.ts:2
 exports[`Sources: should display overide sources' 1`] = `
 "#### Overrides
 
-[SomeClass](../classes/someclass.md).[prop](../classes/someclass.md#prop)
+[SomeClass](../classes/SomeClass.md).[prop](../classes/SomeClass.md#prop)
 
 #### Defined in
 
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/theme.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/theme.spec.ts.snap
index 4c0b8cf77..19db57283 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/theme.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/theme.spec.ts.snap
@@ -5,28 +5,28 @@ Array [
   "modules.md",
   "index.md",
   "modules/breadcrumbs.md",
-  "classes/breadcrumbs.breadcrumbs-1.md",
-  "classes/breadcrumbs.breadcrumbs-1.md#constructor",
-  "classes/breadcrumbs.breadcrumbs-1.md#somemethod",
+  "classes/breadcrumbs.Breadcrumbs.md",
+  "classes/breadcrumbs.Breadcrumbs.md#constructor",
+  "classes/breadcrumbs.Breadcrumbs.md#somemethod",
   "modules/theme.md",
   "modules/theme.md#declarationitema",
   "modules/theme.md#declarationitemb",
   "modules/theme.md#functionitema",
   "modules/theme.md#functionitemb",
-  "modules/theme.namespacea.md",
-  "classes/theme.namespacea.somenestedclass.md",
-  "classes/theme.namespacea.somenestedclass.md#constructor",
-  "modules/theme.namespaceb.md",
-  "enums/theme.enumitema.md",
-  "enums/theme.enumitemb.md",
-  "classes/theme.classitema.md",
-  "classes/theme.classitema.md#constructor",
-  "classes/theme.classitemb.md",
-  "classes/theme.classitemb.md#constructor",
-  "interfaces/theme.interfaceitema.md",
-  "interfaces/theme.interfaceitema.md#prop",
-  "interfaces/theme.interfaceitemb.md",
-  "interfaces/theme.interfaceitemb.md#prop",
+  "modules/theme.namespaceA.md",
+  "classes/theme.namespaceA.SomeNestedClass.md",
+  "classes/theme.namespaceA.SomeNestedClass.md#constructor",
+  "modules/theme.namespaceB.md",
+  "enums/theme.enumItemA.md",
+  "enums/theme.enumItemB.md",
+  "classes/theme.ClassItemA.md",
+  "classes/theme.ClassItemA.md#constructor",
+  "classes/theme.ClassItemB.md",
+  "classes/theme.ClassItemB.md#constructor",
+  "interfaces/theme.InterfaceItemA.md",
+  "interfaces/theme.InterfaceItemA.md#prop",
+  "interfaces/theme.InterfaceItemB.md",
+  "interfaces/theme.InterfaceItemB.md#prop",
 ]
 `;
 
@@ -35,28 +35,28 @@ Array [
   "modules.md",
   "README.md",
   "modules/breadcrumbs.md",
-  "classes/breadcrumbs-breadcrumbs-1.md",
-  "classes/breadcrumbs-breadcrumbs-1.md#constructor",
-  "classes/breadcrumbs-breadcrumbs-1.md#somemethod",
+  "classes/breadcrumbs-Breadcrumbs.md",
+  "classes/breadcrumbs-Breadcrumbs.md#constructor",
+  "classes/breadcrumbs-Breadcrumbs.md#somemethod",
   "modules/theme.md",
   "modules/theme.md#declarationitema",
   "modules/theme.md#declarationitemb",
   "modules/theme.md#functionitema",
   "modules/theme.md#functionitemb",
-  "modules/theme-namespacea.md",
-  "classes/theme-namespacea-somenestedclass.md",
-  "classes/theme-namespacea-somenestedclass.md#constructor",
-  "modules/theme-namespaceb.md",
-  "enums/theme-enumitema.md",
-  "enums/theme-enumitemb.md",
-  "classes/theme-classitema.md",
-  "classes/theme-classitema.md#constructor",
-  "classes/theme-classitemb.md",
-  "classes/theme-classitemb.md#constructor",
-  "interfaces/theme-interfaceitema.md",
-  "interfaces/theme-interfaceitema.md#prop",
-  "interfaces/theme-interfaceitemb.md",
-  "interfaces/theme-interfaceitemb.md#prop",
+  "modules/theme-namespaceA.md",
+  "classes/theme-namespaceA-SomeNestedClass.md",
+  "classes/theme-namespaceA-SomeNestedClass.md#constructor",
+  "modules/theme-namespaceB.md",
+  "enums/theme-enumItemA.md",
+  "enums/theme-enumItemB.md",
+  "classes/theme-ClassItemA.md",
+  "classes/theme-ClassItemA.md#constructor",
+  "classes/theme-ClassItemB.md",
+  "classes/theme-ClassItemB.md#constructor",
+  "interfaces/theme-InterfaceItemA.md",
+  "interfaces/theme-InterfaceItemA.md#prop",
+  "interfaces/theme-InterfaceItemB.md",
+  "interfaces/theme-InterfaceItemB.md#prop",
 ]
 `;
 
@@ -193,13 +193,13 @@ exports[`Theme: (getNavigation) should getNavigation' 1`] = `
    \\"children\\": [
     {
      \\"title\\": \\"namespaceA\\",
-     \\"url\\": \\"modules/namespacea.md\\",
+     \\"url\\": \\"modules/namespaceA.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     },
     {
      \\"title\\": \\"namespaceB\\",
-     \\"url\\": \\"modules/namespaceb.md\\",
+     \\"url\\": \\"modules/namespaceB.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     }
@@ -212,13 +212,13 @@ exports[`Theme: (getNavigation) should getNavigation' 1`] = `
    \\"children\\": [
     {
      \\"title\\": \\"enumItemA\\",
-     \\"url\\": \\"enums/enumitema.md\\",
+     \\"url\\": \\"enums/enumItemA.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     },
     {
      \\"title\\": \\"enumItemB\\",
-     \\"url\\": \\"enums/enumitemb.md\\",
+     \\"url\\": \\"enums/enumItemB.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     }
@@ -231,19 +231,19 @@ exports[`Theme: (getNavigation) should getNavigation' 1`] = `
    \\"children\\": [
     {
      \\"title\\": \\"ClassItemA\\",
-     \\"url\\": \\"classes/classitema.md\\",
+     \\"url\\": \\"classes/ClassItemA.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     },
     {
      \\"title\\": \\"ClassItemB\\",
-     \\"url\\": \\"classes/classitemb.md\\",
+     \\"url\\": \\"classes/ClassItemB.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     },
     {
      \\"title\\": \\"namespaceA.SomeNestedClass\\",
-     \\"url\\": \\"classes/namespacea.somenestedclass.md\\",
+     \\"url\\": \\"classes/namespaceA.SomeNestedClass.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     }
@@ -256,13 +256,13 @@ exports[`Theme: (getNavigation) should getNavigation' 1`] = `
    \\"children\\": [
     {
      \\"title\\": \\"InterfaceItemA\\",
-     \\"url\\": \\"interfaces/interfaceitema.md\\",
+     \\"url\\": \\"interfaces/InterfaceItemA.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     },
     {
      \\"title\\": \\"InterfaceItemB\\",
-     \\"url\\": \\"interfaces/interfaceitemb.md\\",
+     \\"url\\": \\"interfaces/InterfaceItemB.md\\",
      \\"isLabel\\": true,
      \\"children\\": []
     }
@@ -277,28 +277,28 @@ Array [
   "modules.md",
   "README.md",
   "modules/breadcrumbs.md",
-  "classes/breadcrumbs.breadcrumbs-1.md",
-  "classes/breadcrumbs.breadcrumbs-1.md#constructor",
-  "classes/breadcrumbs.breadcrumbs-1.md#somemethod",
+  "classes/breadcrumbs.Breadcrumbs.md",
+  "classes/breadcrumbs.Breadcrumbs.md#constructor",
+  "classes/breadcrumbs.Breadcrumbs.md#somemethod",
   "modules/theme.md",
-  "modules/theme.namespacea.md",
-  "classes/theme.namespacea.somenestedclass.md",
-  "classes/theme.namespacea.somenestedclass.md#constructor",
-  "modules/theme.namespaceb.md",
-  "enums/theme.enumitema.md",
-  "enums/theme.enumitemb.md",
-  "classes/theme.classitema.md",
-  "classes/theme.classitema.md#constructor",
-  "classes/theme.classitemb.md",
-  "classes/theme.classitemb.md#constructor",
-  "interfaces/theme.interfaceitema.md",
-  "interfaces/theme.interfaceitema.md#prop",
-  "interfaces/theme.interfaceitemb.md",
-  "interfaces/theme.interfaceitemb.md#prop",
-  "variables/theme.declarationitema.md",
-  "variables/theme.declarationitemb.md",
-  "functions/theme.functionitema.md",
-  "functions/theme.functionitemb.md",
+  "modules/theme.namespaceA.md",
+  "classes/theme.namespaceA.SomeNestedClass.md",
+  "classes/theme.namespaceA.SomeNestedClass.md#constructor",
+  "modules/theme.namespaceB.md",
+  "enums/theme.enumItemA.md",
+  "enums/theme.enumItemB.md",
+  "classes/theme.ClassItemA.md",
+  "classes/theme.ClassItemA.md#constructor",
+  "classes/theme.ClassItemB.md",
+  "classes/theme.ClassItemB.md#constructor",
+  "interfaces/theme.InterfaceItemA.md",
+  "interfaces/theme.InterfaceItemA.md#prop",
+  "interfaces/theme.InterfaceItemB.md",
+  "interfaces/theme.InterfaceItemB.md#prop",
+  "variables/theme.declarationItemA.md",
+  "variables/theme.declarationItemB.md",
+  "functions/theme.functionItemA.md",
+  "functions/theme.functionItemB.md",
 ]
 `;
 
@@ -306,28 +306,28 @@ exports[`Theme: (getUrls) should getUrls with readme 'none' 1`] = `
 Array [
   "README.md",
   "modules/breadcrumbs.md",
-  "classes/breadcrumbs.breadcrumbs-1.md",
-  "classes/breadcrumbs.breadcrumbs-1.md#constructor",
-  "classes/breadcrumbs.breadcrumbs-1.md#somemethod",
+  "classes/breadcrumbs.Breadcrumbs.md",
+  "classes/breadcrumbs.Breadcrumbs.md#constructor",
+  "classes/breadcrumbs.Breadcrumbs.md#somemethod",
   "modules/theme.md",
   "modules/theme.md#declarationitema",
   "modules/theme.md#declarationitemb",
   "modules/theme.md#functionitema",
   "modules/theme.md#functionitemb",
-  "modules/theme.namespacea.md",
-  "classes/theme.namespacea.somenestedclass.md",
-  "classes/theme.namespacea.somenestedclass.md#constructor",
-  "modules/theme.namespaceb.md",
-  "enums/theme.enumitema.md",
-  "enums/theme.enumitemb.md",
-  "classes/theme.classitema.md",
-  "classes/theme.classitema.md#constructor",
-  "classes/theme.classitemb.md",
-  "classes/theme.classitemb.md#constructor",
-  "interfaces/theme.interfaceitema.md",
-  "interfaces/theme.interfaceitema.md#prop",
-  "interfaces/theme.interfaceitemb.md",
-  "interfaces/theme.interfaceitemb.md#prop",
+  "modules/theme.namespaceA.md",
+  "classes/theme.namespaceA.SomeNestedClass.md",
+  "classes/theme.namespaceA.SomeNestedClass.md#constructor",
+  "modules/theme.namespaceB.md",
+  "enums/theme.enumItemA.md",
+  "enums/theme.enumItemB.md",
+  "classes/theme.ClassItemA.md",
+  "classes/theme.ClassItemA.md#constructor",
+  "classes/theme.ClassItemB.md",
+  "classes/theme.ClassItemB.md#constructor",
+  "interfaces/theme.InterfaceItemA.md",
+  "interfaces/theme.InterfaceItemA.md#prop",
+  "interfaces/theme.InterfaceItemB.md",
+  "interfaces/theme.InterfaceItemB.md#prop",
 ]
 `;
 
@@ -336,27 +336,27 @@ Array [
   "modules.md",
   "README.md",
   "modules/breadcrumbs.md",
-  "classes/breadcrumbs.breadcrumbs-1.md",
-  "classes/breadcrumbs.breadcrumbs-1.md#constructor",
-  "classes/breadcrumbs.breadcrumbs-1.md#somemethod",
+  "classes/breadcrumbs.Breadcrumbs.md",
+  "classes/breadcrumbs.Breadcrumbs.md#constructor",
+  "classes/breadcrumbs.Breadcrumbs.md#somemethod",
   "modules/theme.md",
   "modules/theme.md#declarationitema",
   "modules/theme.md#declarationitemb",
   "modules/theme.md#functionitema",
   "modules/theme.md#functionitemb",
-  "modules/theme.namespacea.md",
-  "classes/theme.namespacea.somenestedclass.md",
-  "classes/theme.namespacea.somenestedclass.md#constructor",
-  "modules/theme.namespaceb.md",
-  "enums/theme.enumitema.md",
-  "enums/theme.enumitemb.md",
-  "classes/theme.classitema.md",
-  "classes/theme.classitema.md#constructor",
-  "classes/theme.classitemb.md",
-  "classes/theme.classitemb.md#constructor",
-  "interfaces/theme.interfaceitema.md",
-  "interfaces/theme.interfaceitema.md#prop",
-  "interfaces/theme.interfaceitemb.md",
-  "interfaces/theme.interfaceitemb.md#prop",
+  "modules/theme.namespaceA.md",
+  "classes/theme.namespaceA.SomeNestedClass.md",
+  "classes/theme.namespaceA.SomeNestedClass.md#constructor",
+  "modules/theme.namespaceB.md",
+  "enums/theme.enumItemA.md",
+  "enums/theme.enumItemB.md",
+  "classes/theme.ClassItemA.md",
+  "classes/theme.ClassItemA.md#constructor",
+  "classes/theme.ClassItemB.md",
+  "classes/theme.ClassItemB.md#constructor",
+  "interfaces/theme.InterfaceItemA.md",
+  "interfaces/theme.InterfaceItemA.md#prop",
+  "interfaces/theme.InterfaceItemB.md",
+  "interfaces/theme.InterfaceItemB.md#prop",
 ]
 `;
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/toc.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/toc.spec.ts.snap
index a07445ba8..feb7a2364 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/toc.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/toc.spec.ts.snap
@@ -5,11 +5,11 @@ exports[`TOC: (default) should display toc for class' 1`] = `
 
 ### Constructors
 
-- [constructor](breadcrumbs.md#constructor)
+- [constructor](Breadcrumbs.md#constructor)
 
 ### Methods
 
-- [someMethod](breadcrumbs.md#somemethod)
+- [someMethod](Breadcrumbs.md#somemethod)
 "
 `;
 
@@ -18,10 +18,10 @@ exports[`TOC: (default) should display toc for module' 1`] = `
 
 ### Constructors
 
-- [constructor](breadcrumbs.md#constructor)
+- [constructor](Breadcrumbs.md#constructor)
 
 ### Methods
 
-- [someMethod](breadcrumbs.md#somemethod)
+- [someMethod](Breadcrumbs.md#somemethod)
 "
 `;
diff --git a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/types.spec.ts.snap b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/types.spec.ts.snap
index 715eb9f6b..077389b3a 100644
--- a/packages/typedoc-plugin-markdown/test/specs/__snapshots__/types.spec.ts.snap
+++ b/packages/typedoc-plugin-markdown/test/specs/__snapshots__/types.spec.ts.snap
@@ -5,7 +5,7 @@ exports[`Types: should compile 'array' type' 1`] = `
 "
 `;
 
-exports[`Types: should compile 'intersection' type' 1`] = `"[\`IntersectionClassA\`](intersectionclassa.md) & [\`IntersectionClassB\`](intersectionclassb.md)"`;
+exports[`Types: should compile 'intersection' type' 1`] = `"[\`IntersectionClassA\`](IntersectionClassA.md) & [\`IntersectionClassB\`](IntersectionClassB.md)"`;
 
 exports[`Types: should compile 'stringLiteral' type' 1`] = `
 "\`\`\\"blue\\"\`\`
diff --git a/packages/typedoc-plugin-markdown/test/specs/breadcrumbs.spec.ts b/packages/typedoc-plugin-markdown/test/specs/breadcrumbs.spec.ts
index 7bccb466e..581bca4ba 100644
--- a/packages/typedoc-plugin-markdown/test/specs/breadcrumbs.spec.ts
+++ b/packages/typedoc-plugin-markdown/test/specs/breadcrumbs.spec.ts
@@ -4,16 +4,13 @@ import { Reflection } from 'typedoc';
 import { TestApp } from '../test-app';
 
 describe(`Breadcrumbs:`, () => {
-  let testApp: TestApp;
   let moduleReflection: Reflection;
   let classReflection: Reflection;
 
-  beforeAll(() => {
-    testApp = new TestApp(['breadcrumbs.ts']);
-  });
-
   describe(`(with readme)`, () => {
+    let testApp: TestApp;
     beforeAll(async () => {
+      testApp = new TestApp(['breadcrumbs.ts']);
       await testApp.bootstrap();
       moduleReflection = testApp.project.children[0];
       classReflection = testApp.project.findReflectionByName('Breadcrumbs');
@@ -59,7 +56,9 @@ describe(`Breadcrumbs:`, () => {
     });
   });
   describe(`(without readme)`, () => {
+    let testApp: TestApp;
     beforeAll(async () => {
+      testApp = new TestApp(['breadcrumbs.ts']);
       await testApp.bootstrap({ readme: 'none' });
       moduleReflection = testApp.project.children[0];
       classReflection = testApp.project.findReflectionByName('Breadcrumbs');
diff --git a/packages/typedoc-plugin-markdown/test/specs/generics.spec.ts b/packages/typedoc-plugin-markdown/test/specs/generics.spec.ts
index 49def848a..aca20c594 100644
--- a/packages/typedoc-plugin-markdown/test/specs/generics.spec.ts
+++ b/packages/typedoc-plugin-markdown/test/specs/generics.spec.ts
@@ -10,12 +10,12 @@ describe(`Generics:`, () => {
   let reflectionTemplate: Handlebars.TemplateDelegate;
 
   beforeAll(() => {
-    testApp = new TestApp(['generics.ts']);
     partial = TestApp.getPartial('member.signature');
     declarationPartial = TestApp.getPartial('member.declaration');
   });
 
   beforeEach(async () => {
+    testApp = new TestApp(['generics.ts']);
     await testApp.bootstrap();
     TestApp.stubPartials([
       'comment',
diff --git a/packages/typedoc-plugin-markdown/test/specs/options.spec.ts b/packages/typedoc-plugin-markdown/test/specs/options.spec.ts
index b61f733aa..b15b9181b 100644
--- a/packages/typedoc-plugin-markdown/test/specs/options.spec.ts
+++ b/packages/typedoc-plugin-markdown/test/specs/options.spec.ts
@@ -3,14 +3,10 @@ import * as Handlebars from 'handlebars';
 import { TestApp } from '../test-app';
 
 describe(`Options:`, () => {
-  let testApp: TestApp;
-
-  beforeAll(() => {
-    testApp = new TestApp(['breadcrumbs.ts']);
-  });
-
   describe(`(defaults)`, () => {
+    let testApp: TestApp;
     beforeAll(async () => {
+      testApp = new TestApp(['breadcrumbs.ts']);
       await testApp.bootstrap({});
     });
 
@@ -39,7 +35,9 @@ describe(`Options:`, () => {
   });
 
   describe(`(with plugin options)`, () => {
+    let testApp: TestApp;
     beforeAll(async () => {
+      testApp = new TestApp(['breadcrumbs.ts']);
       await testApp.bootstrap({
         publicPath: 'test-public-path',
         namedAnchors: true,
diff --git a/packages/typedoc-plugin-markdown/test/specs/plugin.spec.ts b/packages/typedoc-plugin-markdown/test/specs/plugin.spec.ts
index 3967e494f..daa913066 100644
--- a/packages/typedoc-plugin-markdown/test/specs/plugin.spec.ts
+++ b/packages/typedoc-plugin-markdown/test/specs/plugin.spec.ts
@@ -5,14 +5,13 @@ import MarkdownTheme from 'typedoc-plugin-markdown/dist/theme';
 import { TestApp } from '../test-app';
 
 describe(`Plugin:`, () => {
-  let testApp: TestApp;
   const defaultMarkdownThemePath = path.resolve(__dirname, '..', '..', 'dist');
 
-  beforeAll(() => {
-    testApp = new TestApp(['theme.ts']);
-  });
-
   describe(`(load theme)`, () => {
+    let testApp: TestApp;
+    beforeEach(() => {
+      testApp = new TestApp(['theme.ts']);
+    });
     afterEach(() => {
       testApp.app.renderer.theme = undefined;
       testApp.app.renderer.removeComponent('theme');
@@ -21,7 +20,6 @@ describe(`Plugin:`, () => {
     test(`should load markdown theme by default`, async () => {
       await testApp.bootstrap();
       expect(testApp.theme instanceof MarkdownTheme).toBeTruthy();
-      expect(testApp.theme.basePath).toEqual(defaultMarkdownThemePath);
     });
 
     test(`should load custom markdown theme by path'`, async () => {
@@ -35,13 +33,11 @@ describe(`Plugin:`, () => {
         theme: customThemePath,
       });
       expect(testApp.theme instanceof MarkdownTheme).toBeTruthy();
-      expect(testApp.theme.basePath).toEqual(customThemePath);
     });
 
-    test(`should load markdown theme with unrecognised theme'`, async () => {
+    test(`should not load markdown theme with unrecognised theme'`, async () => {
       await testApp.bootstrap({ theme: 'minimal' });
-      expect(testApp.theme instanceof MarkdownTheme).toBeTruthy();
-      expect(testApp.theme.basePath).toEqual(defaultMarkdownThemePath);
+      expect(testApp.theme instanceof MarkdownTheme).toBeFalsy();
     });
   });
 });
diff --git a/packages/typedoc-plugin-markdown/test/specs/reflections.spec.ts b/packages/typedoc-plugin-markdown/test/specs/reflections.spec.ts
index cce431f27..7aa45a18b 100644
--- a/packages/typedoc-plugin-markdown/test/specs/reflections.spec.ts
+++ b/packages/typedoc-plugin-markdown/test/specs/reflections.spec.ts
@@ -3,15 +3,12 @@ import * as Handlebars from 'handlebars';
 import { TestApp } from '../test-app';
 
 describe(`Reflections:`, () => {
-  let testApp: TestApp;
   let reflectionTemplate: Handlebars.TemplateDelegate;
 
-  beforeAll(() => {
-    testApp = new TestApp(['reflections.ts']);
-  });
-
   describe(`(header)`, () => {
+    let testApp: TestApp;
     beforeEach(async () => {
+      testApp = new TestApp(['reflections.ts']);
       await testApp.bootstrap({
         hideBreadcrumbs: false,
         hidePageTitle: true,
@@ -31,7 +28,9 @@ describe(`Reflections:`, () => {
   });
 
   describe(`(template)`, () => {
+    let testApp: TestApp;
     beforeEach(async () => {
+      testApp = new TestApp(['reflections.ts']);
       await testApp.bootstrap({
         hideBreadcrumbs: true,
         hidePageTitle: false,
diff --git a/packages/typedoc-plugin-markdown/test/specs/theme.spec.ts b/packages/typedoc-plugin-markdown/test/specs/theme.spec.ts
index 2fff40276..8a9be31f9 100644
--- a/packages/typedoc-plugin-markdown/test/specs/theme.spec.ts
+++ b/packages/typedoc-plugin-markdown/test/specs/theme.spec.ts
@@ -3,18 +3,16 @@ import * as fs from 'fs';
 import { TestApp } from '../test-app';
 
 describe(`Theme:`, () => {
-  let testApp: TestApp;
-
   describe(`(getNavigation)`, () => {
     test(`should getNavigation'`, async () => {
-      testApp = new TestApp(['theme.ts']);
+      const testApp = new TestApp(['theme.ts']);
       await testApp.bootstrap();
       const navigation = testApp.theme.getNavigation(testApp.project);
       expect(JSON.stringify(navigation, null, 1)).toMatchSnapshot();
     });
 
     test(`should getNavigation for exports'`, async () => {
-      testApp = new TestApp(['theme.ts']);
+      const testApp = new TestApp(['theme.ts']);
       await testApp.bootstrap();
       const navigation = testApp.theme
         .getNavigation(testApp.project)
@@ -23,7 +21,7 @@ describe(`Theme:`, () => {
     });
 
     test(`should getNavigation for exports with readme=none'`, async () => {
-      testApp = new TestApp(['theme.ts']);
+      const testApp = new TestApp(['theme.ts']);
       await testApp.bootstrap({ readme: 'none' });
       const navigation = testApp.theme
         .getNavigation(testApp.project)
@@ -32,7 +30,7 @@ describe(`Theme:`, () => {
     });
 
     test(`should getNavigation for modules'`, async () => {
-      testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
+      const testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
       await testApp.bootstrap();
       const navigation = testApp.theme
         .getNavigation(testApp.project)
@@ -41,7 +39,7 @@ describe(`Theme:`, () => {
     });
 
     test(`should getNavigation for modules with readme=none'`, async () => {
-      testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
+      const testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
       await testApp.bootstrap({ readme: 'none' });
       const navigation = testApp.theme
         .getNavigation(testApp.project)
@@ -51,22 +49,23 @@ describe(`Theme:`, () => {
   });
 
   describe(`(getUrls)`, () => {
-    beforeAll(() => {
-      testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
-    });
+    beforeAll(() => {});
     test(`should getUrls'`, async () => {
+      const testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
       await testApp.bootstrap();
       const urlMappings = testApp.theme.getUrls(testApp.project);
       expect(TestApp.getExpectedUrls(urlMappings)).toMatchSnapshot();
     });
 
     test(`should getUrls with 'allReflectionsHaveOwnDocument' set`, async () => {
+      const testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
       await testApp.bootstrap({ allReflectionsHaveOwnDocument: true });
       const urlMappings = testApp.theme.getUrls(testApp.project);
       expect(TestApp.getExpectedUrls(urlMappings)).toMatchSnapshot();
     });
 
     test(`should getUrls with readme 'none'`, async () => {
+      const testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
       await testApp.bootstrap({ readme: 'none' });
       const urlMappings = testApp.theme.getUrls(testApp.project);
       expect(TestApp.getExpectedUrls(urlMappings)).toMatchSnapshot();
@@ -74,10 +73,8 @@ describe(`Theme:`, () => {
   });
 
   describe(`(filenameSeparator)`, () => {
-    beforeAll(() => {
-      testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
-    });
     test(`should getUrls with custom separator'`, async () => {
+      const testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
       await testApp.bootstrap({ filenameSeparator: '-' });
       const urlMappings = testApp.theme.getUrls(testApp.project);
       expect(TestApp.getExpectedUrls(urlMappings)).toMatchSnapshot();
@@ -86,6 +83,7 @@ describe(`Theme:`, () => {
 
   describe(`(entryDocument)`, () => {
     test(`should getUrls with custom entryDocument'`, async () => {
+      const testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
       await testApp.bootstrap({ entryDocument: 'index.md' });
       const urlMappings = testApp.theme.getUrls(testApp.project);
       expect(TestApp.getExpectedUrls(urlMappings)).toMatchSnapshot();
@@ -93,6 +91,7 @@ describe(`Theme:`, () => {
   });
 
   describe(`(isOutputDirectory)`, () => {
+    let testApp: TestApp;
     beforeAll(() => {
       testApp = new TestApp(['breadcrumbs.ts', 'theme.ts']);
     });
diff --git a/packages/typedoc-plugin-markdown/test/specs/toc.spec.ts b/packages/typedoc-plugin-markdown/test/specs/toc.spec.ts
index 5a3511b64..a688ec05d 100644
--- a/packages/typedoc-plugin-markdown/test/specs/toc.spec.ts
+++ b/packages/typedoc-plugin-markdown/test/specs/toc.spec.ts
@@ -4,16 +4,13 @@ import { Reflection } from 'typedoc';
 import { TestApp } from '../test-app';
 
 describe(`TOC:`, () => {
-  let testApp: TestApp;
   let moduleReflection: Reflection;
   let classReflection: Reflection;
 
-  beforeAll(() => {
-    testApp = new TestApp(['breadcrumbs.ts']);
-  });
-
   describe(`(default)`, () => {
+    let testApp: TestApp;
     beforeAll(async () => {
+      testApp = new TestApp(['breadcrumbs.ts']);
       await testApp.bootstrap();
       moduleReflection = testApp.project.children[0];
       classReflection = testApp.project.findReflectionByName('Breadcrumbs');
@@ -32,7 +29,9 @@ describe(`TOC:`, () => {
     });
   });
   describe(`(hideInPageToc)`, () => {
+    let testApp: TestApp;
     beforeAll(async () => {
+      testApp = new TestApp(['breadcrumbs.ts']);
       await testApp.bootstrap({ hideInPageTOC: true });
       moduleReflection = testApp.project.children[0];
       classReflection = testApp.project.findReflectionByName('Breadcrumbs');
diff --git a/packages/typedoc-plugin-markdown/test/test-app.ts b/packages/typedoc-plugin-markdown/test/test-app.ts
index 5bf73eca0..55e662dd0 100644
--- a/packages/typedoc-plugin-markdown/test/test-app.ts
+++ b/packages/typedoc-plugin-markdown/test/test-app.ts
@@ -5,7 +5,6 @@ import * as Handlebars from 'handlebars';
 import * as tmp from 'tmp';
 import {
   Application,
-  ArgumentsReader,
   DeclarationReflection,
   ProjectReflection,
   Renderer,
@@ -14,6 +13,7 @@ import {
   UrlMapping,
 } from 'typedoc';
 
+import { load } from '../src/index';
 import MarkdownTheme from '../src/theme';
 
 tmp.setGracefulCleanup();
@@ -108,17 +108,15 @@ export class TestApp {
           path.join(__dirname, './stubs/src/' + inputFile),
         )
       : ['./test/stubs/src'];
-    this.app.options.addReader(new ArgumentsReader(0));
+    load(this.app);
     this.app.options.addReader(new TypeDocReader());
     this.app.options.addReader(new TSConfigReader());
-    this.app.options.addReader(new ArgumentsReader(300));
   }
 
   async bootstrap(options: any = {}) {
     this.app.bootstrap({
       logger: 'none',
       entryPoints: this.entryPoints,
-      plugin: [path.join(__dirname, '../dist/index')],
       tsconfig: path.join(__dirname, 'stubs', 'tsconfig.json'),
       ...options,
     });