From ed379ea45edd01b71d754f9d3e808f7da8980ce6 Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 6 Apr 2018 11:43:09 +0200
Subject: [PATCH 01/17] Add paths util

---
 src/index.ts                       |  1 +
 src/lib/utils/paths.ts             | 17 +++++++++++
 src/test/renderer/specs/index.html |  2 ++
 src/test/utils.paths.ts            | 47 ++++++++++++++++++++++++++++++
 4 files changed, 67 insertions(+)
 create mode 100644 src/lib/utils/paths.ts
 create mode 100644 src/test/utils.paths.ts

diff --git a/src/index.ts b/src/index.ts
index a1c3ca875..7241c7b66 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -2,6 +2,7 @@ export { Application } from './lib/application';
 export { CliApplication } from './lib/cli';
 
 export { EventDispatcher, Event } from './lib/utils/events';
+export { pathToMinimatch } from './lib/utils/paths';
 export { resetReflectionID } from './lib/models/reflections/abstract';
 export { normalizePath } from './lib/utils/fs';
 export * from './lib/models/reflections';
diff --git a/src/lib/utils/paths.ts b/src/lib/utils/paths.ts
new file mode 100644
index 000000000..a93984833
--- /dev/null
+++ b/src/lib/utils/paths.ts
@@ -0,0 +1,17 @@
+import * as Path from 'path';
+import { isArray } from 'util';
+import { Minimatch, IMinimatch } from 'minimatch';
+
+function createMinimatch(pattern: string): IMinimatch {
+  if (pattern[0] === '.' || /^\w+(?!:)($|[/\\])/.test(pattern)) {
+    pattern = Path.resolve(pattern);
+  }
+
+  return new Minimatch(pattern, { dot: true });
+}
+
+export function pathToMinimatch(pattern: string | string[]): IMinimatch | IMinimatch[] {
+  return isArray(pattern)
+    ? pattern.map(createMinimatch)
+    : createMinimatch(pattern);
+}
diff --git a/src/test/renderer/specs/index.html b/src/test/renderer/specs/index.html
index 37e333b0d..c0173c72f 100644
--- a/src/test/renderer/specs/index.html
+++ b/src/test/renderer/specs/index.html
@@ -127,6 +127,8 @@ <h4 id="typescript-compiler">TypeScript compiler</h4>
 					Specify module code generation: &quot;commonjs&quot;, &quot;amd&quot;, &quot;system&quot; or &quot;umd&quot;.</li>
 					<li><code>--target &lt;ES3, ES5, or ES6&gt;</code><br>
 					Specify ECMAScript target version: &quot;ES3&quot; (default), &quot;ES5&quot; or &quot;ES6&quot;</li>
+					<li><code>--tsconfig &lt;path/to/tsconfig.json&gt;</code><br>
+					Specify a typescript config file that should be loaded. If not specified TypeDoc will look for &#39;tsconfig.json&#39; in the current directory.</li>
 				</ul>
 				<h4 id="theming">Theming</h4>
 				<ul>
diff --git a/src/test/utils.paths.ts b/src/test/utils.paths.ts
new file mode 100644
index 000000000..bff6b2565
--- /dev/null
+++ b/src/test/utils.paths.ts
@@ -0,0 +1,47 @@
+import * as Path from 'path';
+import { Minimatch, IMinimatch } from 'minimatch';
+
+import isEqual = require('lodash/isEqual');
+import Assert = require('assert');
+
+import { pathToMinimatch } from '..';
+
+describe('Paths', () => {
+  describe('pathToMinimatch', () => {
+    it('Converts a path to a Minimatch expression', () => {
+      const mm = pathToMinimatch('/some/path/**');
+      Assert(mm instanceof Minimatch, 'Path not coverted to Minimatch');
+    });
+
+    it('Converts an array of paths to an array of Minimatch expressions', () => {
+      const mms = <IMinimatch[]> pathToMinimatch(['/some/path/**', '**/another/path/**', './relative/**/path']);
+      Assert(Array.isArray(mms), 'Didn\'t return an array');
+
+      const allAreMm = mms.every((mm) => mm instanceof Minimatch);
+      Assert(allAreMm, 'Not all paths are coverted to Minimatch');
+    });
+
+    it('Minimatch can match absolute paths expressions', () => {
+      const paths = ['/unix/absolute/**/path', 'C:/Windows/absolute/*/path', '**/arbitrary/path/**'];
+      const mms: string[] = (<IMinimatch[]> pathToMinimatch(paths))
+      .map(({ pattern }) => pattern);
+
+      Assert(isEqual(mms, paths), `Patterns have been altered:\nMMS: ${mms}\nPaths: ${paths}`);
+    });
+
+    it('Minimatch can match relative to the project root', () => {
+      const paths = ['./relative/**/path', '../parent/*/path', 'no/dot/relative/**/path/*', '.dot/relative/**/path/*'];
+      const absPaths = paths.map((path) => Path.resolve(path).replace(/\\/g, '/'));
+      const mms: string[] = (<IMinimatch[]> pathToMinimatch(paths))
+      .map(({ pattern }) => pattern);
+
+      Assert(isEqual(mms, absPaths), `Project root have not been added to paths:\nMMS: ${mms}\nPaths: ${absPaths}`);
+    });
+
+    it('Minimatch matches dot files', () => {
+      const mm = <IMinimatch> pathToMinimatch('/some/path/**');
+      Assert(mm.match('/some/path/.dot/dir'), 'Didn\'t match .dot path');
+      Assert(mm.match('/some/path/normal/dir'), 'Didn\'t match normal path');
+    });
+  });
+});

From 668d104822ef9520c2289966f69293020ec488b3 Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 6 Apr 2018 11:46:53 +0200
Subject: [PATCH 02/17] Add general minimatch function to `externalPattern`

- Also allowed it to take multiple path expressions
---
 src/lib/converter/context.ts   | 13 +++++++------
 src/lib/converter/converter.ts |  5 +++--
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/lib/converter/context.ts b/src/lib/converter/context.ts
index 6678c1776..1aaafcb4f 100644
--- a/src/lib/converter/context.ts
+++ b/src/lib/converter/context.ts
@@ -1,8 +1,10 @@
 import * as ts from 'typescript';
-import { Minimatch, IMinimatch } from 'minimatch';
+import { IMinimatch } from 'minimatch';
 
 import { Logger } from '../utils/loggers';
+import { pathToMinimatch } from '../utils/paths';
 import { Reflection, ProjectReflection, ContainerReflection, Type } from '../models/index';
+
 import { createTypeParameter } from './factories/type-parameter';
 import { Converter } from './converter';
 
@@ -93,7 +95,7 @@ export class Context {
     /**
      * The pattern that should be used to flag external source files.
      */
-    private externalPattern: IMinimatch;
+    private externalPattern: Array<IMinimatch>;
 
     /**
      * Create a new Context instance.
@@ -114,7 +116,7 @@ export class Context {
         this.scope = project;
 
         if (converter.externalPattern) {
-            this.externalPattern = new Minimatch(converter.externalPattern);
+            this.externalPattern = <IMinimatch[]> pathToMinimatch(converter.externalPattern);
         }
     }
 
@@ -216,10 +218,9 @@ export class Context {
      * @param callback  The callback that should be executed.
      */
     withSourceFile(node: ts.SourceFile, callback: Function) {
-        const externalPattern = this.externalPattern;
         let isExternal = this.fileNames.indexOf(node.fileName) === -1;
-        if (externalPattern) {
-            isExternal = isExternal || externalPattern.match(node.fileName);
+        if (!isExternal && this.externalPattern) {
+            isExternal = this.externalPattern.some(mm => mm.match(node.fileName));
         }
 
         if (isExternal && this.converter.excludeExternals) {
diff --git a/src/lib/converter/converter.ts b/src/lib/converter/converter.ts
index 5a02111e6..e13209159 100644
--- a/src/lib/converter/converter.ts
+++ b/src/lib/converter/converter.ts
@@ -42,9 +42,10 @@ export class Converter extends ChildableComponent<Application, ConverterComponen
 
     @Option({
         name: 'externalPattern',
-        help: 'Define a pattern for files that should be considered being external.'
+        help: 'Define patterns for files that should be considered being external.',
+        type: ParameterType.Array
     })
-    externalPattern: string;
+    externalPattern: Array<string>;
 
     @Option({
         name: 'includeDeclarations',

From cd7970d6b9cbe689354073f7ef78e90cfd5bf009 Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 6 Apr 2018 11:48:21 +0200
Subject: [PATCH 03/17] Add general minimatch function to `exclude`

---
 src/lib/application.ts | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/lib/application.ts b/src/lib/application.ts
index ba72dff84..b66e8619d 100644
--- a/src/lib/application.ts
+++ b/src/lib/application.ts
@@ -9,13 +9,14 @@
 import * as Path from 'path';
 import * as FS from 'fs';
 import * as typescript from 'typescript';
-import { Minimatch, IMinimatch } from 'minimatch';
+import { IMinimatch } from 'minimatch';
 
 import { Converter } from './converter/index';
 import { Renderer } from './output/renderer';
 import { Serializer } from './serialization';
 import { ProjectReflection } from './models/index';
 import { Logger, ConsoleLogger, CallbackLogger, PluginHost, writeFile } from './utils/index';
+import { pathToMinimatch } from './utils/paths';
 
 import { AbstractComponent, ChildableComponent, Component, Option } from './utils/component';
 import { Options, OptionsReadMode, OptionsReadResult } from './utils/options/index';
@@ -248,7 +249,10 @@ export class Application extends ChildableComponent<Application, AbstractCompone
      */
     public expandInputFiles(inputFiles?: string[]): string[] {
         let files: string[] = [];
-        const exclude: Array<IMinimatch> = this.exclude ? this.exclude.map(pattern => new Minimatch(pattern)) : [];
+
+        const exclude: IMinimatch[] = this.exclude
+          ? <IMinimatch[]> pathToMinimatch(this.exclude)
+          : [];
 
         function isExcluded(fileName: string): boolean {
             return exclude.some(mm => mm.match(fileName));

From 3c80f10a3f9c0d94c463fb9934cb186031c5345a Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 6 Apr 2018 11:49:13 +0200
Subject: [PATCH 04/17] Fix typedoc.js(on) options file finding

---
 src/lib/utils/options/readers/typedoc.ts | 48 ++++++++++++++++++------
 1 file changed, 36 insertions(+), 12 deletions(-)

diff --git a/src/lib/utils/options/readers/typedoc.ts b/src/lib/utils/options/readers/typedoc.ts
index a03e8df11..8b9261856 100644
--- a/src/lib/utils/options/readers/typedoc.ts
+++ b/src/lib/utils/options/readers/typedoc.ts
@@ -31,30 +31,54 @@ export class TypedocReader extends OptionsComponent {
             return;
         }
 
+        let file: string;
+
         if (TypedocReader.OPTIONS_KEY in event.data) {
-            this.load(event, Path.resolve(event.data[TypedocReader.OPTIONS_KEY]));
+          let opts = event.data[TypedocReader.OPTIONS_KEY];
+
+          if (opts[0] === '.') { opts = Path.resolve(opts); }
+
+          file = this.findTypedocFile(opts);
+
+          if (!FS.existsSync(file)) {
+            event.addError('The options file could not be found with the given path %s.', opts);
+            return;
+          }
         } else if (this.application.isCLI) {
-            const file = Path.resolve('typedoc.js');
-            if (FS.existsSync(file)) {
-                this.load(event, file);
-            }
+          file = this.findTypedocFile();
         }
+
+        file && this.load(event, file);
+    }
+
+    /**
+     * Search for the typedoc.js or typedoc.json file from the given path
+     *
+     * @param  path Path to the typedoc.(js|json) file. If path is a directory
+     *   typedoc file will be attempted to be found at the root of this path
+     * @return the typedoc.(js|json) file path or undefined
+     */
+    findTypedocFile(path: string = process.cwd()): string | undefined {
+      let file: string;
+
+      if (/typedoc\.js(on)?$/.test(path)) {
+        file = path;
+      } else {
+        file = Path.join(path, 'typedoc.js');
+        if (!FS.existsSync(file)) { file += 'on'; }
+      }
+
+      return FS.existsSync(file) ? file : undefined;
     }
 
     /**
      * Load the specified option file.
      *
+     * @param event The event object from the DISCOVER event.
      * @param optionFile  The absolute path and file name of the option file.
-     * @param ignoreUnknownArgs  Should unknown arguments be ignored? If so the parser
-     *   will simply skip all unknown arguments.
      * @returns TRUE on success, otherwise FALSE.
      */
     load(event: DiscoverEvent, optionFile: string) {
-        if (!FS.existsSync(optionFile)) {
-            event.addError('The option file %s does not exist.', optionFile);
-            return;
-        }
-
         let data = require(optionFile);
         if (typeof data === 'function') {
             data = data(this.application);

From ac777fcadec407f8afcc2b659e929fb73aa59860 Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 6 Apr 2018 11:49:36 +0200
Subject: [PATCH 05/17] Optimize tsconfig.json file finding

---
 src/lib/utils/options/readers/tsconfig.ts | 40 +++++++++++++----------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/src/lib/utils/options/readers/tsconfig.ts b/src/lib/utils/options/readers/tsconfig.ts
index d0430bb9e..9b12bef0a 100644
--- a/src/lib/utils/options/readers/tsconfig.ts
+++ b/src/lib/utils/options/readers/tsconfig.ts
@@ -37,24 +37,33 @@ export class TSConfigReader extends OptionsComponent {
     onDiscover(event: DiscoverEvent) {
         // Do nothing until were fetching options
         if (event.mode !== OptionsReadMode.Fetch) {
-            return;
+          return;
         }
 
+        let file: string;
+
         if (TSConfigReader.OPTIONS_KEY in event.data) {
-            this.load(event, Path.resolve(event.data[TSConfigReader.OPTIONS_KEY]));
+          const tsconfig = event.data[TSConfigReader.OPTIONS_KEY];
+
+          file = /tsconfig\.json$/.test(tsconfig)
+            ? Path.resolve(tsconfig)
+            : ts.findConfigFile(tsconfig, ts.sys.fileExists);
+
+          if (!file || !FS.existsSync(file)) {
+              event.addError('The tsconfig file %s does not exist.', file);
+              return;
+          }
         } else if (TSConfigReader.PROJECT_KEY in event.data) {
-            // The `project` option may be a directory or file, so use TS to find it
-            let file: string = ts.findConfigFile(event.data[TSConfigReader.PROJECT_KEY], ts.sys.fileExists);
-            // If file is undefined, we found no file to load.
-            if (file) {
-                this.load(event, file);
-            }
+          // The `project` option may be a directory or file, so use TS to find it
+          file = ts.findConfigFile(event.data[TSConfigReader.PROJECT_KEY], ts.sys.fileExists);
         } else if (this.application.isCLI) {
-            let file: string = ts.findConfigFile('.', ts.sys.fileExists);
-            // If file is undefined, we found no file to load.
-            if (file) {
-                this.load(event, file);
-            }
+          // No file or directory has been specified so find the file in the root of the project
+          file = ts.findConfigFile('.', ts.sys.fileExists);
+        }
+
+        // If file is undefined, we found no file to load.
+        if (file) {
+          this.load(event, file);
         }
     }
 
@@ -65,11 +74,6 @@ export class TSConfigReader extends OptionsComponent {
      * @param fileName  The absolute path and file name of the tsconfig file.
      */
     load(event: DiscoverEvent, fileName: string) {
-        if (!FS.existsSync(fileName)) {
-            event.addError('The tsconfig file %s does not exist.', fileName);
-            return;
-        }
-
         const { config } = ts.readConfigFile(fileName, ts.sys.readFile);
         if (config === undefined) {
             event.addError('The tsconfig file %s does not contain valid JSON.', fileName);

From 772822767a80f4ea79175e25d8ab8a2aa1df67ff Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 6 Apr 2018 11:53:01 +0200
Subject: [PATCH 06/17] Update dependencies

---
 package-lock.json | 38 +++++++++++++++++++-------------------
 package.json      | 24 ++++++++++++------------
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 2913fb470..c3372212d 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -38,9 +38,9 @@
       "integrity": "sha512-y5x0XD/WXDaGSyiTaTcKS4FurULJtSiYbGTeQd0m2LYZGBcZZ/7fM6t5H/DzeUF+kv8y6UfmF6yJABQsHcp9VQ=="
     },
     "@types/lodash": {
-      "version": "4.14.104",
-      "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.14.104.tgz",
-      "integrity": "sha512-ufQcVg4daO8xQ5kopxRHanqFdL4AI7ondQkV+2f+7mz3gvp0LkBx2zBRC6hfs3T87mzQFmf5Fck7Fi145Ul6NQ=="
+      "version": "4.14.106",
+      "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.14.106.tgz",
+      "integrity": "sha512-tOSvCVrvSqFZ4A/qrqqm6p37GZoawsZtoR0SJhlF7EonNZUgrn8FfT+RNQ11h+NUpMt6QVe36033f3qEKBwfWA=="
     },
     "@types/marked": {
       "version": "0.3.0",
@@ -53,9 +53,9 @@
       "integrity": "sha512-tHq6qdbT9U1IRSGf14CL0pUlULksvY9OZ+5eEgl1N7t+OA3tGvNpxJCzuKQlsNgCVwbAs670L1vcVQi8j9HjnA=="
     },
     "@types/mocha": {
-      "version": "2.2.48",
-      "resolved": "https://registry.npmjs.org/@types/mocha/-/mocha-2.2.48.tgz",
-      "integrity": "sha512-nlK/iyETgafGli8Zh9zJVCTicvU3iajSkRwOh3Hhiva598CMqNJ4NcVCGMTGKpGpTYj/9R8RLzS9NAykSSCqGw==",
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/@types/mocha/-/mocha-5.0.0.tgz",
+      "integrity": "sha512-ZS0vBV7Jn5Z/Q4T3VXauEKMDCV8nWOtJJg90OsDylkYJiQwcWtKuLzohWzrthBkerUF7DLMmJcwOPEP0i/AOXw==",
       "dev": true
     },
     "@types/node": {
@@ -690,7 +690,7 @@
       "dev": true,
       "optional": true,
       "requires": {
-        "nan": "2.7.0"
+        "nan": "2.10.0"
       }
     },
     "gaze": {
@@ -1436,9 +1436,9 @@
       "dev": true
     },
     "marked": {
-      "version": "0.3.17",
-      "resolved": "https://registry.npmjs.org/marked/-/marked-0.3.17.tgz",
-      "integrity": "sha512-+AKbNsjZl6jFfLPwHhWmGTqE009wTKn3RTmn9K8oUKHrX/abPJjtcRtXpYB/FFrwPJRUA86LX/de3T0knkPCmQ=="
+      "version": "0.3.19",
+      "resolved": "https://registry.npmjs.org/marked/-/marked-0.3.19.tgz",
+      "integrity": "sha512-ea2eGWOqNxPcXv8dyERdSr/6FmzvWwzjMxpfGB/sbMccXoct+xY+YukPD+QTUZwyvK7BZwcr4m21WBOW41pAkg=="
     },
     "media-typer": {
       "version": "0.3.0",
@@ -1550,9 +1550,9 @@
       }
     },
     "mocha": {
-      "version": "5.0.4",
-      "resolved": "https://registry.npmjs.org/mocha/-/mocha-5.0.4.tgz",
-      "integrity": "sha512-nMOpAPFosU1B4Ix1jdhx5e3q7XO55ic5a8cgYvW27CequcEY+BabS0kUVL1Cw1V5PuVHZWeNRWFLmEPexo79VA==",
+      "version": "5.0.5",
+      "resolved": "https://registry.npmjs.org/mocha/-/mocha-5.0.5.tgz",
+      "integrity": "sha512-3MM3UjZ5p8EJrYpG7s+29HAI9G7sTzKEe4+w37Dg0QP7qL4XGsV+Q2xet2cE37AqdgN1OtYQB6Vl98YiPV3PgA==",
       "dev": true,
       "requires": {
         "browser-stdout": "1.3.1",
@@ -1612,9 +1612,9 @@
       "dev": true
     },
     "nan": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/nan/-/nan-2.7.0.tgz",
-      "integrity": "sha1-2Vv3IeyHfgjbJ27T/G63j5CDrUY=",
+      "version": "2.10.0",
+      "resolved": "https://registry.npmjs.org/nan/-/nan-2.10.0.tgz",
+      "integrity": "sha512-bAdJv7fBLhWC+/Bls0Oza+mvTaNQtP+1RyhhhvD95pgUJz6XM5IzgmxOkItJ9tkoCiplvAnXI1tNmmUD/eScyA==",
       "dev": true,
       "optional": true
     },
@@ -2306,9 +2306,9 @@
       "integrity": "sha1-bcJDPnjti+qOiHo6zeLzF4W9Yic="
     },
     "typescript": {
-      "version": "2.7.2",
-      "resolved": "https://registry.npmjs.org/typescript/-/typescript-2.7.2.tgz",
-      "integrity": "sha512-p5TCYZDAO0m4G344hD+wx/LATebLWZNkkh2asWUFqSsD2OrDNhbAHuSjobrmsUmdzjJjEeZVU9g1h3O6vpstnw=="
+      "version": "2.8.1",
+      "resolved": "https://registry.npmjs.org/typescript/-/typescript-2.8.1.tgz",
+      "integrity": "sha512-Ao/f6d/4EPLq0YwzsQz8iXflezpTkQzqAyenTiw4kCUGr1uPiFLC3+fZ+gMZz6eeI/qdRUqvC+HxIJzUAzEFdg=="
     },
     "uglify-js": {
       "version": "2.8.29",
diff --git a/package.json b/package.json
index 8e6b3bc34..8b38e33bf 100644
--- a/package.json
+++ b/package.json
@@ -33,34 +33,34 @@
     "@types/fs-extra": "5.0.1",
     "@types/handlebars": "4.0.36",
     "@types/highlight.js": "9.12.2",
-    "@types/lodash": "4.14.104",
+    "@types/lodash": "4.14.106",
     "@types/marked": "0.3.0",
     "@types/minimatch": "3.0.3",
     "@types/shelljs": "0.7.8",
     "fs-extra": "^5.0.0",
-    "handlebars": "^4.0.6",
-    "highlight.js": "^9.0.0",
+    "handlebars": "^4.0.11",
+    "highlight.js": "^9.12.0",
     "lodash": "^4.17.5",
-    "marked": "^0.3.17",
-    "minimatch": "^3.0.0",
+    "marked": "^0.3.19",
+    "minimatch": "^3.0.4",
     "progress": "^2.0.0",
     "shelljs": "^0.8.1",
     "typedoc-default-themes": "^0.5.0",
-    "typescript": "2.7.2"
+    "typescript": "2.8.1"
   },
   "devDependencies": {
-    "@types/mocha": "2.2.48",
+    "@types/mocha": "5.0.0",
     "grunt": "^1.0.2",
     "grunt-cli": "^1.2.0",
-    "grunt-contrib-clean": "^1.0.0",
+    "grunt-contrib-clean": "^1.1.0",
     "grunt-contrib-copy": "^1.0.0",
     "grunt-contrib-watch": "^1.0.0",
-    "grunt-mocha-istanbul": "^5.0.1",
-    "grunt-string-replace": "^1.2.0",
+    "grunt-mocha-istanbul": "^5.0.2",
+    "grunt-string-replace": "^1.3.1",
     "grunt-ts": "^5.5.1",
     "grunt-tslint": "^5.0.1",
-    "istanbul": "^0.4.1",
-    "mocha": "^5.0.4",
+    "istanbul": "^0.4.5",
+    "mocha": "^5.0.5",
     "tslint": "^5.9.1"
   },
   "files": [

From 422785132c5d5d6d0e90e69e476272e740f0c4bd Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 6 Apr 2018 15:01:41 +0200
Subject: [PATCH 07/17] Add unit tests for matching paths

---
 src/lib/utils/paths.ts  |  4 ++--
 src/test/utils.paths.ts | 30 ++++++++++++++++++++++--------
 2 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/src/lib/utils/paths.ts b/src/lib/utils/paths.ts
index a93984833..cffa48397 100644
--- a/src/lib/utils/paths.ts
+++ b/src/lib/utils/paths.ts
@@ -3,11 +3,11 @@ import { isArray } from 'util';
 import { Minimatch, IMinimatch } from 'minimatch';
 
 function createMinimatch(pattern: string): IMinimatch {
-  if (pattern[0] === '.' || /^\w+(?!:)($|[/\\])/.test(pattern)) {
+  if (pattern[0] === '.' || pattern[0] === '/' || /^\w+(?!:)($|[/\\])/.test(pattern)) {
     pattern = Path.resolve(pattern);
   }
 
-  return new Minimatch(pattern, { dot: true });
+  return new Minimatch(pattern.replace(/[\\]/g, '/'), { dot: true });
 }
 
 export function pathToMinimatch(pattern: string | string[]): IMinimatch | IMinimatch[] {
diff --git a/src/test/utils.paths.ts b/src/test/utils.paths.ts
index bff6b2565..f509c9ef5 100644
--- a/src/test/utils.paths.ts
+++ b/src/test/utils.paths.ts
@@ -6,6 +6,9 @@ import Assert = require('assert');
 
 import { pathToMinimatch } from '..';
 
+// Used to ensure uniform path cross OS
+const absolutePath = (path: string) => Path.resolve(path).replace(/[\\]/g, '/');
+
 describe('Paths', () => {
   describe('pathToMinimatch', () => {
     it('Converts a path to a Minimatch expression', () => {
@@ -23,25 +26,36 @@ describe('Paths', () => {
 
     it('Minimatch can match absolute paths expressions', () => {
       const paths = ['/unix/absolute/**/path', 'C:/Windows/absolute/*/path', '**/arbitrary/path/**'];
-      const mms: string[] = (<IMinimatch[]> pathToMinimatch(paths))
-      .map(({ pattern }) => pattern);
+      const mms = (<IMinimatch[]> pathToMinimatch(paths));
+      const patterns = mms.map(({ pattern }) => pattern);
+      const comparePaths = [...paths];
+      comparePaths[0] = absolutePath(comparePaths[0]);
+
+      Assert(isEqual(patterns, comparePaths), `Patterns have been altered:\nMMS: ${patterns}\nPaths: ${comparePaths}`);
 
-      Assert(isEqual(mms, paths), `Patterns have been altered:\nMMS: ${mms}\nPaths: ${paths}`);
+      Assert(mms[0].match(absolutePath('/unix/absolute/some/sub/dir/path')), 'Din\'t match unix path');
+      Assert(mms[1].match('C:/Windows/absolute/test/path'), 'Din\'t match windows path');
+      Assert(mms[2].match(absolutePath('/some/deep/arbitrary/path/leading/nowhere')), 'Din\'t match arbitrary path');
     });
 
     it('Minimatch can match relative to the project root', () => {
       const paths = ['./relative/**/path', '../parent/*/path', 'no/dot/relative/**/path/*', '.dot/relative/**/path/*'];
       const absPaths = paths.map((path) => Path.resolve(path).replace(/\\/g, '/'));
-      const mms: string[] = (<IMinimatch[]> pathToMinimatch(paths))
-      .map(({ pattern }) => pattern);
+      const mms = (<IMinimatch[]> pathToMinimatch(paths));
+      const patterns = mms.map(({ pattern }) => pattern);
+
+      Assert(isEqual(patterns, absPaths), `Project root have not been added to paths:\nMMS: ${patterns}\nPaths: ${absPaths}`);
 
-      Assert(isEqual(mms, absPaths), `Project root have not been added to paths:\nMMS: ${mms}\nPaths: ${absPaths}`);
+      Assert(mms[0].match(Path.resolve('relative/some/sub/dir/path')), 'Din\'t match relative path');
+      Assert(mms[1].match(Path.resolve('../parent/dir/path')), 'Din\'t match parent path');
+      Assert(mms[2].match(Path.resolve('no/dot/relative/some/sub/dir/path/test')), 'Din\'t match no dot path');
+      Assert(mms[3].match(Path.resolve('.dot/relative/some/sub/dir/path/test')), 'Din\'t match dot path');
     });
 
     it('Minimatch matches dot files', () => {
       const mm = <IMinimatch> pathToMinimatch('/some/path/**');
-      Assert(mm.match('/some/path/.dot/dir'), 'Didn\'t match .dot path');
-      Assert(mm.match('/some/path/normal/dir'), 'Didn\'t match normal path');
+      Assert(mm.match(absolutePath('/some/path/.dot/dir')), 'Didn\'t match .dot path');
+      Assert(mm.match(absolutePath('/some/path/normal/dir')), 'Didn\'t match normal path');
     });
   });
 });

From 4b9ca6c5ac0feb3e6c260b85eb5043d035f91f8b Mon Sep 17 00:00:00 2001
From: aciccarello <a3chic9@gmail.com>
Date: Wed, 11 Apr 2018 21:45:18 -0600
Subject: [PATCH 08/17] style tweaks

---
 src/lib/utils/options/readers/tsconfig.ts | 36 ++++++++++++-----------
 src/lib/utils/options/readers/typedoc.ts  | 35 ++++++++++++----------
 2 files changed, 38 insertions(+), 33 deletions(-)

diff --git a/src/lib/utils/options/readers/tsconfig.ts b/src/lib/utils/options/readers/tsconfig.ts
index 9b12bef0a..249db7de6 100644
--- a/src/lib/utils/options/readers/tsconfig.ts
+++ b/src/lib/utils/options/readers/tsconfig.ts
@@ -37,33 +37,35 @@ export class TSConfigReader extends OptionsComponent {
     onDiscover(event: DiscoverEvent) {
         // Do nothing until were fetching options
         if (event.mode !== OptionsReadMode.Fetch) {
-          return;
+            return;
         }
 
         let file: string;
 
         if (TSConfigReader.OPTIONS_KEY in event.data) {
-          const tsconfig = event.data[TSConfigReader.OPTIONS_KEY];
-
-          file = /tsconfig\.json$/.test(tsconfig)
-            ? Path.resolve(tsconfig)
-            : ts.findConfigFile(tsconfig, ts.sys.fileExists);
-
-          if (!file || !FS.existsSync(file)) {
-              event.addError('The tsconfig file %s does not exist.', file);
-              return;
-          }
+            const tsconfig = event.data[TSConfigReader.OPTIONS_KEY];
+
+            if (/tsconfig\.json$/.test(tsconfig)) {
+                file = Path.resolve(tsconfig);
+            } else {
+                file = ts.findConfigFile(tsconfig, ts.sys.fileExists);
+            }
+
+            if (!file || !FS.existsSync(file)) {
+                event.addError('The tsconfig file %s does not exist.', file);
+                return;
+            }
         } else if (TSConfigReader.PROJECT_KEY in event.data) {
-          // The `project` option may be a directory or file, so use TS to find it
-          file = ts.findConfigFile(event.data[TSConfigReader.PROJECT_KEY], ts.sys.fileExists);
+            // The `project` option may be a directory or file, so use TS to find it
+            file = ts.findConfigFile(event.data[TSConfigReader.PROJECT_KEY], ts.sys.fileExists);
         } else if (this.application.isCLI) {
-          // No file or directory has been specified so find the file in the root of the project
-          file = ts.findConfigFile('.', ts.sys.fileExists);
+            // No file or directory has been specified so find the file in the root of the project
+            file = ts.findConfigFile('.', ts.sys.fileExists);
         }
 
         // If file is undefined, we found no file to load.
         if (file) {
-          this.load(event, file);
+            this.load(event, file);
         }
     }
 
@@ -76,7 +78,7 @@ export class TSConfigReader extends OptionsComponent {
     load(event: DiscoverEvent, fileName: string) {
         const { config } = ts.readConfigFile(fileName, ts.sys.readFile);
         if (config === undefined) {
-            event.addError('The tsconfig file %s does not contain valid JSON.', fileName);
+            event.addError('No valid tsconfig file found.', fileName);
             return;
         }
         if (!_.isPlainObject(config)) {
diff --git a/src/lib/utils/options/readers/typedoc.ts b/src/lib/utils/options/readers/typedoc.ts
index 8b9261856..05bb68458 100644
--- a/src/lib/utils/options/readers/typedoc.ts
+++ b/src/lib/utils/options/readers/typedoc.ts
@@ -34,18 +34,20 @@ export class TypedocReader extends OptionsComponent {
         let file: string;
 
         if (TypedocReader.OPTIONS_KEY in event.data) {
-          let opts = event.data[TypedocReader.OPTIONS_KEY];
+            let opts = event.data[TypedocReader.OPTIONS_KEY];
 
-          if (opts[0] === '.') { opts = Path.resolve(opts); }
+            if (opts && opts[0] === '.') {
+                opts = Path.resolve(opts);
+            }
 
-          file = this.findTypedocFile(opts);
+            file = this.findTypedocFile(opts);
 
-          if (!FS.existsSync(file)) {
-            event.addError('The options file could not be found with the given path %s.', opts);
-            return;
-          }
+            if (!FS.existsSync(file)) {
+                event.addError('The options file could not be found with the given path %s.', opts);
+                return;
+            }
         } else if (this.application.isCLI) {
-          file = this.findTypedocFile();
+            file = this.findTypedocFile();
         }
 
         file && this.load(event, file);
@@ -59,16 +61,17 @@ export class TypedocReader extends OptionsComponent {
      * @return the typedoc.(js|json) file path or undefined
      */
     findTypedocFile(path: string = process.cwd()): string | undefined {
-      let file: string;
+        if (/typedoc\.js(on)?$/.test(path)) {
+            return path;
+        }
 
-      if (/typedoc\.js(on)?$/.test(path)) {
-        file = path;
-      } else {
-        file = Path.join(path, 'typedoc.js');
-        if (!FS.existsSync(file)) { file += 'on'; }
-      }
+        let file = Path.join(path, 'typedoc.js');
+        if (FS.existsSync(file)) {
+            return file;
+        }
 
-      return FS.existsSync(file) ? file : undefined;
+        file += 'on'; // look for JSON file
+        return FS.existsSync(file) ? file : undefined;
     }
 
     /**

From a6bb62d9a30fd70e2422799bfb29a40621eb8ee1 Mon Sep 17 00:00:00 2001
From: aciccarello <a3chic9@gmail.com>
Date: Wed, 11 Apr 2018 22:09:52 -0600
Subject: [PATCH 09/17] add file name back into tsconfig load error

---
 src/lib/utils/options/readers/tsconfig.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/lib/utils/options/readers/tsconfig.ts b/src/lib/utils/options/readers/tsconfig.ts
index 249db7de6..02d3d707d 100644
--- a/src/lib/utils/options/readers/tsconfig.ts
+++ b/src/lib/utils/options/readers/tsconfig.ts
@@ -78,7 +78,7 @@ export class TSConfigReader extends OptionsComponent {
     load(event: DiscoverEvent, fileName: string) {
         const { config } = ts.readConfigFile(fileName, ts.sys.readFile);
         if (config === undefined) {
-            event.addError('No valid tsconfig file found.', fileName);
+            event.addError('No valid tsconfig file found for %s.', fileName);
             return;
         }
         if (!_.isPlainObject(config)) {

From b9d45ef5401a4bb8958c4a781a34b308e5c3ccfe Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 13 Apr 2018 13:56:27 +0200
Subject: [PATCH 10/17] Revert "Update dependencies"

This reverts commit 772822767a80f4ea79175e25d8ab8a2aa1df67ff.
---
 package-lock.json | 38 +++++++++++++++++++-------------------
 package.json      | 24 ++++++++++++------------
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index c3372212d..2913fb470 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -38,9 +38,9 @@
       "integrity": "sha512-y5x0XD/WXDaGSyiTaTcKS4FurULJtSiYbGTeQd0m2LYZGBcZZ/7fM6t5H/DzeUF+kv8y6UfmF6yJABQsHcp9VQ=="
     },
     "@types/lodash": {
-      "version": "4.14.106",
-      "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.14.106.tgz",
-      "integrity": "sha512-tOSvCVrvSqFZ4A/qrqqm6p37GZoawsZtoR0SJhlF7EonNZUgrn8FfT+RNQ11h+NUpMt6QVe36033f3qEKBwfWA=="
+      "version": "4.14.104",
+      "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.14.104.tgz",
+      "integrity": "sha512-ufQcVg4daO8xQ5kopxRHanqFdL4AI7ondQkV+2f+7mz3gvp0LkBx2zBRC6hfs3T87mzQFmf5Fck7Fi145Ul6NQ=="
     },
     "@types/marked": {
       "version": "0.3.0",
@@ -53,9 +53,9 @@
       "integrity": "sha512-tHq6qdbT9U1IRSGf14CL0pUlULksvY9OZ+5eEgl1N7t+OA3tGvNpxJCzuKQlsNgCVwbAs670L1vcVQi8j9HjnA=="
     },
     "@types/mocha": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmjs.org/@types/mocha/-/mocha-5.0.0.tgz",
-      "integrity": "sha512-ZS0vBV7Jn5Z/Q4T3VXauEKMDCV8nWOtJJg90OsDylkYJiQwcWtKuLzohWzrthBkerUF7DLMmJcwOPEP0i/AOXw==",
+      "version": "2.2.48",
+      "resolved": "https://registry.npmjs.org/@types/mocha/-/mocha-2.2.48.tgz",
+      "integrity": "sha512-nlK/iyETgafGli8Zh9zJVCTicvU3iajSkRwOh3Hhiva598CMqNJ4NcVCGMTGKpGpTYj/9R8RLzS9NAykSSCqGw==",
       "dev": true
     },
     "@types/node": {
@@ -690,7 +690,7 @@
       "dev": true,
       "optional": true,
       "requires": {
-        "nan": "2.10.0"
+        "nan": "2.7.0"
       }
     },
     "gaze": {
@@ -1436,9 +1436,9 @@
       "dev": true
     },
     "marked": {
-      "version": "0.3.19",
-      "resolved": "https://registry.npmjs.org/marked/-/marked-0.3.19.tgz",
-      "integrity": "sha512-ea2eGWOqNxPcXv8dyERdSr/6FmzvWwzjMxpfGB/sbMccXoct+xY+YukPD+QTUZwyvK7BZwcr4m21WBOW41pAkg=="
+      "version": "0.3.17",
+      "resolved": "https://registry.npmjs.org/marked/-/marked-0.3.17.tgz",
+      "integrity": "sha512-+AKbNsjZl6jFfLPwHhWmGTqE009wTKn3RTmn9K8oUKHrX/abPJjtcRtXpYB/FFrwPJRUA86LX/de3T0knkPCmQ=="
     },
     "media-typer": {
       "version": "0.3.0",
@@ -1550,9 +1550,9 @@
       }
     },
     "mocha": {
-      "version": "5.0.5",
-      "resolved": "https://registry.npmjs.org/mocha/-/mocha-5.0.5.tgz",
-      "integrity": "sha512-3MM3UjZ5p8EJrYpG7s+29HAI9G7sTzKEe4+w37Dg0QP7qL4XGsV+Q2xet2cE37AqdgN1OtYQB6Vl98YiPV3PgA==",
+      "version": "5.0.4",
+      "resolved": "https://registry.npmjs.org/mocha/-/mocha-5.0.4.tgz",
+      "integrity": "sha512-nMOpAPFosU1B4Ix1jdhx5e3q7XO55ic5a8cgYvW27CequcEY+BabS0kUVL1Cw1V5PuVHZWeNRWFLmEPexo79VA==",
       "dev": true,
       "requires": {
         "browser-stdout": "1.3.1",
@@ -1612,9 +1612,9 @@
       "dev": true
     },
     "nan": {
-      "version": "2.10.0",
-      "resolved": "https://registry.npmjs.org/nan/-/nan-2.10.0.tgz",
-      "integrity": "sha512-bAdJv7fBLhWC+/Bls0Oza+mvTaNQtP+1RyhhhvD95pgUJz6XM5IzgmxOkItJ9tkoCiplvAnXI1tNmmUD/eScyA==",
+      "version": "2.7.0",
+      "resolved": "https://registry.npmjs.org/nan/-/nan-2.7.0.tgz",
+      "integrity": "sha1-2Vv3IeyHfgjbJ27T/G63j5CDrUY=",
       "dev": true,
       "optional": true
     },
@@ -2306,9 +2306,9 @@
       "integrity": "sha1-bcJDPnjti+qOiHo6zeLzF4W9Yic="
     },
     "typescript": {
-      "version": "2.8.1",
-      "resolved": "https://registry.npmjs.org/typescript/-/typescript-2.8.1.tgz",
-      "integrity": "sha512-Ao/f6d/4EPLq0YwzsQz8iXflezpTkQzqAyenTiw4kCUGr1uPiFLC3+fZ+gMZz6eeI/qdRUqvC+HxIJzUAzEFdg=="
+      "version": "2.7.2",
+      "resolved": "https://registry.npmjs.org/typescript/-/typescript-2.7.2.tgz",
+      "integrity": "sha512-p5TCYZDAO0m4G344hD+wx/LATebLWZNkkh2asWUFqSsD2OrDNhbAHuSjobrmsUmdzjJjEeZVU9g1h3O6vpstnw=="
     },
     "uglify-js": {
       "version": "2.8.29",
diff --git a/package.json b/package.json
index 8b38e33bf..8e6b3bc34 100644
--- a/package.json
+++ b/package.json
@@ -33,34 +33,34 @@
     "@types/fs-extra": "5.0.1",
     "@types/handlebars": "4.0.36",
     "@types/highlight.js": "9.12.2",
-    "@types/lodash": "4.14.106",
+    "@types/lodash": "4.14.104",
     "@types/marked": "0.3.0",
     "@types/minimatch": "3.0.3",
     "@types/shelljs": "0.7.8",
     "fs-extra": "^5.0.0",
-    "handlebars": "^4.0.11",
-    "highlight.js": "^9.12.0",
+    "handlebars": "^4.0.6",
+    "highlight.js": "^9.0.0",
     "lodash": "^4.17.5",
-    "marked": "^0.3.19",
-    "minimatch": "^3.0.4",
+    "marked": "^0.3.17",
+    "minimatch": "^3.0.0",
     "progress": "^2.0.0",
     "shelljs": "^0.8.1",
     "typedoc-default-themes": "^0.5.0",
-    "typescript": "2.8.1"
+    "typescript": "2.7.2"
   },
   "devDependencies": {
-    "@types/mocha": "5.0.0",
+    "@types/mocha": "2.2.48",
     "grunt": "^1.0.2",
     "grunt-cli": "^1.2.0",
-    "grunt-contrib-clean": "^1.1.0",
+    "grunt-contrib-clean": "^1.0.0",
     "grunt-contrib-copy": "^1.0.0",
     "grunt-contrib-watch": "^1.0.0",
-    "grunt-mocha-istanbul": "^5.0.2",
-    "grunt-string-replace": "^1.3.1",
+    "grunt-mocha-istanbul": "^5.0.1",
+    "grunt-string-replace": "^1.2.0",
     "grunt-ts": "^5.5.1",
     "grunt-tslint": "^5.0.1",
-    "istanbul": "^0.4.5",
-    "mocha": "^5.0.5",
+    "istanbul": "^0.4.1",
+    "mocha": "^5.0.4",
     "tslint": "^5.9.1"
   },
   "files": [

From 28c5e2218414ccac0afff27a2131c27dbff8eca4 Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 13 Apr 2018 17:55:04 +0200
Subject: [PATCH 11/17] Force 4 spaces as indent for the TS Lint

---
 tslint.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tslint.json b/tslint.json
index 25c3c4f50..a3692696a 100644
--- a/tslint.json
+++ b/tslint.json
@@ -7,7 +7,7 @@
 		"curly": true,
 		"eofline": true,
 		"forin": false,
-		"indent": [ true, "spaces" ],
+		"indent": [ true, "spaces", 4 ],
 		"interface-name": [ true, "never-prefix" ],
 		"jsdoc-format": true,
 		"label-position": true,

From f98996bcbcb0623422440079146d872f68314613 Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 13 Apr 2018 18:01:07 +0200
Subject: [PATCH 12/17] createMinimatch fixed

- Renamed from `pathToMinimatch`
- Added overload methods for easier usage (no need for explicit casting) and clarification
- Updated how absolute and relative paths are checked
- Fixed indentation
---
 src/index.ts                 |  2 +-
 src/lib/application.ts       |  7 +++----
 src/lib/converter/context.ts |  4 ++--
 src/lib/utils/paths.ts       | 29 ++++++++++++++++++++---------
 src/test/utils.paths.ts      | 35 ++++++++++++++++++++---------------
 5 files changed, 46 insertions(+), 31 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index 7241c7b66..36c8fb168 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -2,7 +2,7 @@ export { Application } from './lib/application';
 export { CliApplication } from './lib/cli';
 
 export { EventDispatcher, Event } from './lib/utils/events';
-export { pathToMinimatch } from './lib/utils/paths';
+export { createMinimatch } from './lib/utils/paths';
 export { resetReflectionID } from './lib/models/reflections/abstract';
 export { normalizePath } from './lib/utils/fs';
 export * from './lib/models/reflections';
diff --git a/src/lib/application.ts b/src/lib/application.ts
index b66e8619d..0aad2777a 100644
--- a/src/lib/application.ts
+++ b/src/lib/application.ts
@@ -9,14 +9,13 @@
 import * as Path from 'path';
 import * as FS from 'fs';
 import * as typescript from 'typescript';
-import { IMinimatch } from 'minimatch';
 
 import { Converter } from './converter/index';
 import { Renderer } from './output/renderer';
 import { Serializer } from './serialization';
 import { ProjectReflection } from './models/index';
 import { Logger, ConsoleLogger, CallbackLogger, PluginHost, writeFile } from './utils/index';
-import { pathToMinimatch } from './utils/paths';
+import { createMinimatch } from './utils/paths';
 
 import { AbstractComponent, ChildableComponent, Component, Option } from './utils/component';
 import { Options, OptionsReadMode, OptionsReadResult } from './utils/options/index';
@@ -250,8 +249,8 @@ export class Application extends ChildableComponent<Application, AbstractCompone
     public expandInputFiles(inputFiles?: string[]): string[] {
         let files: string[] = [];
 
-        const exclude: IMinimatch[] = this.exclude
-          ? <IMinimatch[]> pathToMinimatch(this.exclude)
+        const exclude = this.exclude
+          ? createMinimatch(this.exclude)
           : [];
 
         function isExcluded(fileName: string): boolean {
diff --git a/src/lib/converter/context.ts b/src/lib/converter/context.ts
index 1aaafcb4f..5953c6fbb 100644
--- a/src/lib/converter/context.ts
+++ b/src/lib/converter/context.ts
@@ -2,7 +2,7 @@ import * as ts from 'typescript';
 import { IMinimatch } from 'minimatch';
 
 import { Logger } from '../utils/loggers';
-import { pathToMinimatch } from '../utils/paths';
+import { createMinimatch } from '../utils/paths';
 import { Reflection, ProjectReflection, ContainerReflection, Type } from '../models/index';
 
 import { createTypeParameter } from './factories/type-parameter';
@@ -116,7 +116,7 @@ export class Context {
         this.scope = project;
 
         if (converter.externalPattern) {
-            this.externalPattern = <IMinimatch[]> pathToMinimatch(converter.externalPattern);
+            this.externalPattern = createMinimatch(converter.externalPattern);
         }
     }
 
diff --git a/src/lib/utils/paths.ts b/src/lib/utils/paths.ts
index cffa48397..3fcb55add 100644
--- a/src/lib/utils/paths.ts
+++ b/src/lib/utils/paths.ts
@@ -2,16 +2,27 @@ import * as Path from 'path';
 import { isArray } from 'util';
 import { Minimatch, IMinimatch } from 'minimatch';
 
-function createMinimatch(pattern: string): IMinimatch {
-  if (pattern[0] === '.' || pattern[0] === '/' || /^\w+(?!:)($|[/\\])/.test(pattern)) {
-    pattern = Path.resolve(pattern);
-  }
+function convertToMinimatch(pattern: string): IMinimatch {
+    // Ensure uniform absolute path cross OS
+    // (POSIX would resolve c:/path to /path/to/repo/c:/path without this check)
+    if (Path.isAbsolute(pattern) && Path.sep === '/') {
+        pattern = pattern.replace(/^\w:/, '');
+    }
 
-  return new Minimatch(pattern.replace(/[\\]/g, '/'), { dot: true });
+    if (pattern[0] !== '*') {
+        // pattern path is resolved even if it is an absolute path,
+        // to ensure correct format for the current OS
+        pattern = Path.resolve(pattern);
+    }
+
+    // Unify the path slashes before creating the minimatch, for more relyable matching
+    return new Minimatch(pattern.replace(/[\\]/g, '/'), { dot: true });
 }
 
-export function pathToMinimatch(pattern: string | string[]): IMinimatch | IMinimatch[] {
-  return isArray(pattern)
-    ? pattern.map(createMinimatch)
-    : createMinimatch(pattern);
+export function createMinimatch(pattern: string[]): IMinimatch[];
+export function createMinimatch(pattern: string): IMinimatch;
+export function createMinimatch(pattern: string | string[]): IMinimatch | IMinimatch[] {
+    return isArray(pattern)
+        ? pattern.map(convertToMinimatch)
+        : convertToMinimatch(pattern);
 }
diff --git a/src/test/utils.paths.ts b/src/test/utils.paths.ts
index f509c9ef5..ce7532991 100644
--- a/src/test/utils.paths.ts
+++ b/src/test/utils.paths.ts
@@ -1,23 +1,23 @@
 import * as Path from 'path';
-import { Minimatch, IMinimatch } from 'minimatch';
+import { Minimatch } from 'minimatch';
 
 import isEqual = require('lodash/isEqual');
 import Assert = require('assert');
 
-import { pathToMinimatch } from '..';
+import { createMinimatch } from '..';
 
 // Used to ensure uniform path cross OS
-const absolutePath = (path: string) => Path.resolve(path).replace(/[\\]/g, '/');
+const absolutePath = (path: string) => Path.resolve(path.replace(/^\w:/, '')).replace(/[\\]/g, '/');
 
 describe('Paths', () => {
-  describe('pathToMinimatch', () => {
+  describe('createMinimatch', () => {
     it('Converts a path to a Minimatch expression', () => {
-      const mm = pathToMinimatch('/some/path/**');
+      const mm = createMinimatch('/some/path/**');
       Assert(mm instanceof Minimatch, 'Path not coverted to Minimatch');
     });
 
     it('Converts an array of paths to an array of Minimatch expressions', () => {
-      const mms = <IMinimatch[]> pathToMinimatch(['/some/path/**', '**/another/path/**', './relative/**/path']);
+      const mms = createMinimatch(['/some/path/**', '**/another/path/**', './relative/**/path']);
       Assert(Array.isArray(mms), 'Didn\'t return an array');
 
       const allAreMm = mms.every((mm) => mm instanceof Minimatch);
@@ -25,23 +25,28 @@ describe('Paths', () => {
     });
 
     it('Minimatch can match absolute paths expressions', () => {
-      const paths = ['/unix/absolute/**/path', 'C:/Windows/absolute/*/path', '**/arbitrary/path/**'];
-      const mms = (<IMinimatch[]> pathToMinimatch(paths));
+      const paths = ['/unix/absolute/**/path', '\\windows\\alternative\\absolute\\path', 'C:\\Windows\\absolute\\*\\path', '**/arbitrary/path/**'];
+      const mms = createMinimatch(paths);
       const patterns = mms.map(({ pattern }) => pattern);
-      const comparePaths = [...paths];
-      comparePaths[0] = absolutePath(comparePaths[0]);
+      const comparePaths = [
+        absolutePath('/unix/absolute/**/path'),
+        absolutePath('/windows/alternative/absolute/path'),
+        absolutePath('/Windows/absolute/*/path'),
+        '**/arbitrary/path/**'
+      ];
 
       Assert(isEqual(patterns, comparePaths), `Patterns have been altered:\nMMS: ${patterns}\nPaths: ${comparePaths}`);
 
       Assert(mms[0].match(absolutePath('/unix/absolute/some/sub/dir/path')), 'Din\'t match unix path');
-      Assert(mms[1].match('C:/Windows/absolute/test/path'), 'Din\'t match windows path');
-      Assert(mms[2].match(absolutePath('/some/deep/arbitrary/path/leading/nowhere')), 'Din\'t match arbitrary path');
+      Assert(mms[1].match(absolutePath('/windows/alternative/absolute/path')), 'Din\'t match windows alternative path');
+      Assert(mms[2].match(absolutePath('/Windows/absolute/test/path')), 'Din\'t match windows path');
+      Assert(mms[3].match(absolutePath('/some/deep/arbitrary/path/leading/nowhere')), 'Din\'t match arbitrary path');
     });
 
     it('Minimatch can match relative to the project root', () => {
       const paths = ['./relative/**/path', '../parent/*/path', 'no/dot/relative/**/path/*', '.dot/relative/**/path/*'];
-      const absPaths = paths.map((path) => Path.resolve(path).replace(/\\/g, '/'));
-      const mms = (<IMinimatch[]> pathToMinimatch(paths));
+      const absPaths = paths.map((path) => absolutePath(path));
+      const mms = createMinimatch(paths);
       const patterns = mms.map(({ pattern }) => pattern);
 
       Assert(isEqual(patterns, absPaths), `Project root have not been added to paths:\nMMS: ${patterns}\nPaths: ${absPaths}`);
@@ -53,7 +58,7 @@ describe('Paths', () => {
     });
 
     it('Minimatch matches dot files', () => {
-      const mm = <IMinimatch> pathToMinimatch('/some/path/**');
+      const mm = createMinimatch('/some/path/**');
       Assert(mm.match(absolutePath('/some/path/.dot/dir')), 'Didn\'t match .dot path');
       Assert(mm.match(absolutePath('/some/path/normal/dir')), 'Didn\'t match normal path');
     });

From a2340122cf8e98558f2512f2603c25a1e0cc9db8 Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Fri, 13 Apr 2018 18:01:36 +0200
Subject: [PATCH 13/17] updated @types/mocha to match current mocha version

---
 package-lock.json | 6 +++---
 package.json      | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 2913fb470..76f87e5dc 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -53,9 +53,9 @@
       "integrity": "sha512-tHq6qdbT9U1IRSGf14CL0pUlULksvY9OZ+5eEgl1N7t+OA3tGvNpxJCzuKQlsNgCVwbAs670L1vcVQi8j9HjnA=="
     },
     "@types/mocha": {
-      "version": "2.2.48",
-      "resolved": "https://registry.npmjs.org/@types/mocha/-/mocha-2.2.48.tgz",
-      "integrity": "sha512-nlK/iyETgafGli8Zh9zJVCTicvU3iajSkRwOh3Hhiva598CMqNJ4NcVCGMTGKpGpTYj/9R8RLzS9NAykSSCqGw==",
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/@types/mocha/-/mocha-5.0.0.tgz",
+      "integrity": "sha512-ZS0vBV7Jn5Z/Q4T3VXauEKMDCV8nWOtJJg90OsDylkYJiQwcWtKuLzohWzrthBkerUF7DLMmJcwOPEP0i/AOXw==",
       "dev": true
     },
     "@types/node": {
diff --git a/package.json b/package.json
index 8e6b3bc34..10a0d9d1c 100644
--- a/package.json
+++ b/package.json
@@ -49,7 +49,7 @@
     "typescript": "2.7.2"
   },
   "devDependencies": {
-    "@types/mocha": "2.2.48",
+    "@types/mocha": "^5.0.0",
     "grunt": "^1.0.2",
     "grunt-cli": "^1.2.0",
     "grunt-contrib-clean": "^1.0.0",

From 2a6557f72b3b7088bd784abb7023e38a929e58ba Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Tue, 17 Apr 2018 11:27:08 +0200
Subject: [PATCH 14/17] CreateMinimatch always assumes array of strings +
 single star paths are relative

---
 src/lib/utils/paths.ts  | 37 +++++++++++++++----------------------
 src/test/utils.paths.ts | 10 +++-------
 2 files changed, 18 insertions(+), 29 deletions(-)

diff --git a/src/lib/utils/paths.ts b/src/lib/utils/paths.ts
index 3fcb55add..cb7849c8f 100644
--- a/src/lib/utils/paths.ts
+++ b/src/lib/utils/paths.ts
@@ -1,28 +1,21 @@
 import * as Path from 'path';
-import { isArray } from 'util';
 import { Minimatch, IMinimatch } from 'minimatch';
 
-function convertToMinimatch(pattern: string): IMinimatch {
-    // Ensure uniform absolute path cross OS
-    // (POSIX would resolve c:/path to /path/to/repo/c:/path without this check)
-    if (Path.isAbsolute(pattern) && Path.sep === '/') {
-        pattern = pattern.replace(/^\w:/, '');
-    }
+export function createMinimatch(patterns: string[]): IMinimatch[] {
+    return patterns.map((pattern: string): IMinimatch => {
+        // Ensure uniform absolute path cross OS
+        // (POSIX would resolve c:/path to /path/to/repo/c:/path without this check)
+        if (Path.isAbsolute(pattern) && Path.sep === '/') {
+            pattern = pattern.replace(/^\w:/, '');
+        }
 
-    if (pattern[0] !== '*') {
-        // pattern path is resolved even if it is an absolute path,
-        // to ensure correct format for the current OS
-        pattern = Path.resolve(pattern);
-    }
+        // pattern paths not starting with '**' are resolved even if it is an
+        // absolute path, to ensure correct format for the current OS
+        if (pattern.substr(0, 2) !== '**') {
+            pattern = Path.resolve(pattern);
+        }
 
-    // Unify the path slashes before creating the minimatch, for more relyable matching
-    return new Minimatch(pattern.replace(/[\\]/g, '/'), { dot: true });
-}
-
-export function createMinimatch(pattern: string[]): IMinimatch[];
-export function createMinimatch(pattern: string): IMinimatch;
-export function createMinimatch(pattern: string | string[]): IMinimatch | IMinimatch[] {
-    return isArray(pattern)
-        ? pattern.map(convertToMinimatch)
-        : convertToMinimatch(pattern);
+        // Unify the path slashes before creating the minimatch, for more relyable matching
+        return new Minimatch(pattern.replace(/[\\]/g, '/'), { dot: true });
+    });
 }
diff --git a/src/test/utils.paths.ts b/src/test/utils.paths.ts
index ce7532991..3f2f74eb1 100644
--- a/src/test/utils.paths.ts
+++ b/src/test/utils.paths.ts
@@ -11,11 +11,6 @@ const absolutePath = (path: string) => Path.resolve(path.replace(/^\w:/, '')).re
 
 describe('Paths', () => {
   describe('createMinimatch', () => {
-    it('Converts a path to a Minimatch expression', () => {
-      const mm = createMinimatch('/some/path/**');
-      Assert(mm instanceof Minimatch, 'Path not coverted to Minimatch');
-    });
-
     it('Converts an array of paths to an array of Minimatch expressions', () => {
       const mms = createMinimatch(['/some/path/**', '**/another/path/**', './relative/**/path']);
       Assert(Array.isArray(mms), 'Didn\'t return an array');
@@ -44,7 +39,7 @@ describe('Paths', () => {
     });
 
     it('Minimatch can match relative to the project root', () => {
-      const paths = ['./relative/**/path', '../parent/*/path', 'no/dot/relative/**/path/*', '.dot/relative/**/path/*'];
+      const paths = ['./relative/**/path', '../parent/*/path', 'no/dot/relative/**/path/*', '*/subdir/**/path/*', '.dot/relative/**/path/*'];
       const absPaths = paths.map((path) => absolutePath(path));
       const mms = createMinimatch(paths);
       const patterns = mms.map(({ pattern }) => pattern);
@@ -54,11 +49,12 @@ describe('Paths', () => {
       Assert(mms[0].match(Path.resolve('relative/some/sub/dir/path')), 'Din\'t match relative path');
       Assert(mms[1].match(Path.resolve('../parent/dir/path')), 'Din\'t match parent path');
       Assert(mms[2].match(Path.resolve('no/dot/relative/some/sub/dir/path/test')), 'Din\'t match no dot path');
+      Assert(mms[2].match(Path.resolve('some/subdir/path/test')), 'Din\'t match single star path');
       Assert(mms[3].match(Path.resolve('.dot/relative/some/sub/dir/path/test')), 'Din\'t match dot path');
     });
 
     it('Minimatch matches dot files', () => {
-      const mm = createMinimatch('/some/path/**');
+      const mm = createMinimatch(['/some/path/**'])[0];
       Assert(mm.match(absolutePath('/some/path/.dot/dir')), 'Didn\'t match .dot path');
       Assert(mm.match(absolutePath('/some/path/normal/dir')), 'Didn\'t match normal path');
     });

From 91bc957108bb567840afffd42bff756b759dfdad Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Tue, 17 Apr 2018 11:56:29 +0200
Subject: [PATCH 15/17] Correct createMinimatch unit test

---
 src/test/utils.paths.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/test/utils.paths.ts b/src/test/utils.paths.ts
index 3f2f74eb1..db9cae108 100644
--- a/src/test/utils.paths.ts
+++ b/src/test/utils.paths.ts
@@ -49,8 +49,8 @@ describe('Paths', () => {
       Assert(mms[0].match(Path.resolve('relative/some/sub/dir/path')), 'Din\'t match relative path');
       Assert(mms[1].match(Path.resolve('../parent/dir/path')), 'Din\'t match parent path');
       Assert(mms[2].match(Path.resolve('no/dot/relative/some/sub/dir/path/test')), 'Din\'t match no dot path');
-      Assert(mms[2].match(Path.resolve('some/subdir/path/test')), 'Din\'t match single star path');
-      Assert(mms[3].match(Path.resolve('.dot/relative/some/sub/dir/path/test')), 'Din\'t match dot path');
+      Assert(mms[3].match(Path.resolve('some/subdir/path/here')), 'Din\'t match single star path');
+      Assert(mms[4].match(Path.resolve('.dot/relative/some/sub/dir/path/test')), 'Din\'t match dot path');
     });
 
     it('Minimatch matches dot files', () => {

From 2cf1f5f48d41f5bc6c695a5c9074d5edf161ed53 Mon Sep 17 00:00:00 2001
From: Toke Voltelen <toke.voltelen@yoomap.fr>
Date: Wed, 25 Apr 2018 23:33:18 +0200
Subject: [PATCH 16/17] Correct posix pathing

---
 src/lib/utils/paths.ts | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/lib/utils/paths.ts b/src/lib/utils/paths.ts
index cb7849c8f..3f82b24db 100644
--- a/src/lib/utils/paths.ts
+++ b/src/lib/utils/paths.ts
@@ -1,13 +1,12 @@
 import * as Path from 'path';
 import { Minimatch, IMinimatch } from 'minimatch';
 
+const unix = Path.sep === '/';
+
 export function createMinimatch(patterns: string[]): IMinimatch[] {
     return patterns.map((pattern: string): IMinimatch => {
-        // Ensure uniform absolute path cross OS
-        // (POSIX would resolve c:/path to /path/to/repo/c:/path without this check)
-        if (Path.isAbsolute(pattern) && Path.sep === '/') {
-            pattern = pattern.replace(/^\w:/, '');
-        }
+        // Ensure correct pathing on unix, by transforming `\` to `/` and remvoing any `X:/` fromt he path
+        if (unix) { pattern = pattern.replace(/[\\]/g, '/').replace(/^\w:/, ''); }
 
         // pattern paths not starting with '**' are resolved even if it is an
         // absolute path, to ensure correct format for the current OS
@@ -15,7 +14,10 @@ export function createMinimatch(patterns: string[]): IMinimatch[] {
             pattern = Path.resolve(pattern);
         }
 
+        // On Windows we transform `\` to `/` to unify the way paths are intepreted
+        if (!unix) { pattern = pattern.replace(/[\\]/g, '/'); }
+
         // Unify the path slashes before creating the minimatch, for more relyable matching
-        return new Minimatch(pattern.replace(/[\\]/g, '/'), { dot: true });
+        return new Minimatch(pattern, { dot: true });
     });
 }

From e5ed318c391ae2324339baa057c012367e1d395e Mon Sep 17 00:00:00 2001
From: Gerrit Birkeland <gerrit@gerritbirkeland.com>
Date: Sun, 28 Oct 2018 08:31:57 -0600
Subject: [PATCH 17/17] Resolve build errors

Strict null checks required a few changes to code changed by this PR.
---
 src/lib/converter/context.ts              | 2 +-
 src/lib/converter/converter.ts            | 2 +-
 src/lib/utils/options/readers/tsconfig.ts | 4 ++--
 src/lib/utils/options/readers/typedoc.ts  | 4 ++--
 src/test/renderer/specs/index.html        | 2 +-
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/lib/converter/context.ts b/src/lib/converter/context.ts
index 40cd5a144..b2da96fb1 100644
--- a/src/lib/converter/context.ts
+++ b/src/lib/converter/context.ts
@@ -95,7 +95,7 @@ export class Context {
     /**
      * The pattern that should be used to flag external source files.
      */
-    private externalPattern: Array<IMinimatch>;
+    private externalPattern?: Array<IMinimatch>;
 
     /**
      * Create a new Context instance.
diff --git a/src/lib/converter/converter.ts b/src/lib/converter/converter.ts
index e9c4b85a1..c22680ce6 100644
--- a/src/lib/converter/converter.ts
+++ b/src/lib/converter/converter.ts
@@ -45,7 +45,7 @@ export class Converter extends ChildableComponent<Application, ConverterComponen
         help: 'Define patterns for files that should be considered being external.',
         type: ParameterType.Array
     })
-    externalPattern: Array<string>;
+    externalPattern!: Array<string>;
 
     @Option({
         name: 'includeDeclarations',
diff --git a/src/lib/utils/options/readers/tsconfig.ts b/src/lib/utils/options/readers/tsconfig.ts
index 0b1d3f878..30bac190a 100644
--- a/src/lib/utils/options/readers/tsconfig.ts
+++ b/src/lib/utils/options/readers/tsconfig.ts
@@ -40,7 +40,7 @@ export class TSConfigReader extends OptionsComponent {
             return;
         }
 
-        let file: string;
+        let file: string | undefined;
 
         if (TSConfigReader.OPTIONS_KEY in event.data) {
             const tsconfig = event.data[TSConfigReader.OPTIONS_KEY];
@@ -52,7 +52,7 @@ export class TSConfigReader extends OptionsComponent {
             }
 
             if (!file || !FS.existsSync(file)) {
-                event.addError('The tsconfig file %s does not exist.', file);
+                event.addError('The tsconfig file %s does not exist.', file || '');
                 return;
             }
         } else if (TSConfigReader.PROJECT_KEY in event.data) {
diff --git a/src/lib/utils/options/readers/typedoc.ts b/src/lib/utils/options/readers/typedoc.ts
index 7b5ef41a1..2ff821f1d 100644
--- a/src/lib/utils/options/readers/typedoc.ts
+++ b/src/lib/utils/options/readers/typedoc.ts
@@ -31,7 +31,7 @@ export class TypedocReader extends OptionsComponent {
             return;
         }
 
-        let file: string;
+        let file: string | undefined;
 
         if (TypedocReader.OPTIONS_KEY in event.data) {
             let opts = event.data[TypedocReader.OPTIONS_KEY];
@@ -42,7 +42,7 @@ export class TypedocReader extends OptionsComponent {
 
             file = this.findTypedocFile(opts);
 
-            if (!FS.existsSync(file)) {
+            if (!file || !FS.existsSync(file)) {
                 event.addError('The options file could not be found with the given path %s.', opts);
                 return;
             }
diff --git a/src/test/renderer/specs/index.html b/src/test/renderer/specs/index.html
index 988295860..4e7522cef 100644
--- a/src/test/renderer/specs/index.html
+++ b/src/test/renderer/specs/index.html
@@ -203,4 +203,4 @@ <h2>Legend</h2>
 <script src="assets/js/main.js"></script>
 <script>if (location.protocol == 'file:') document.write('<script src="assets/js/search.js"><' + '/script>');</script>
 </body>
-</html>
+</html>
\ No newline at end of file