[BUG] Navigation is broken with watch mode

Overview of the issue

If a file has changed the navigation on the left is broken.

Operating System, Node.js, npm, compodoc version(s)

Compodoc console output

1.1.2
Typescript version : 2.8.1
Node.js version : v7.4.0
Operating system : macOS High Sierra

Angular configuration, a package.json file in the root folder

{
  "name": "My App",
  "version": "0.0.0",
  "license": "MIT",
  "scripts": {
    "ng": "ng",
    "start": "ng serve",
    "build": "ng build --prod",
    "test": "ng test",
    "lint": "ng lint",
    "e2e": "ng e2e",
    "compodoc": "./node_modules/.bin/compodoc -p src/tsconfig.app.json -a src/assets -a mockups -n 'My App - Angular documentation' --includes additional-doc",
    "compodoc:watch": "./node_modules/.bin/compodoc -p src/tsconfig.app.json -a src/assets -a mockups -n 'My App - Angular documentation' --includes additional-doc -w -s",
    "compodoc:serve": "./node_modules/.bin/compodoc -p src/tsconfig.app.json -a src/assets -a mockups -n 'My App - Angular documentation' --includes additional-doc -s",
    "compodoc:help": "./node_modules/.bin/compodoc -p src/tsconfig.app.json -a src/assets -a mockups -n 'My App - Angular documentation' --includes additional-doc -h",
    "storybook": "start-storybook -p 9001 -c storybook"
  },
  "private": true,
  "dependencies": {
    "@angular/animations": "^5.2.9",
    "@angular/common": "^5.2.9",
    "@angular/compiler": "^5.2.9",
    "@angular/core": "^5.2.9",
    "@angular/forms": "^5.2.9",
    "@angular/http": "^5.2.9",
    "@angular/platform-browser": "^5.2.9",
    "@angular/platform-browser-dynamic": "^5.2.9",
    "@angular/router": "^5.2.9",
    "@ng-bootstrap/ng-bootstrap": "^1.1.0",
    "@ngx-translate/core": "^9.1.1",
    "@ngx-translate/http-loader": "^2.0.1",
    "bootstrap": "^4.0.0",
    "core-js": "^2.4.1",
    "jquery": "^3.3.1",
    "popper.js": "^1.14.3",
    "material-design-icons": "1",
    "rxjs": "^5.5.8",
    "zone.js": "^0.8.19"
  },
  "devDependencies": {
    "@angular/cli": "^1.7.3",
    "@angular/compiler-cli": "^5.2.9",
    "@angular/language-service": "^5.2.9",
    "@compodoc/compodoc": "^1.1.1",
    "@storybook/addon-actions": "^3.4.2",
    "@storybook/addon-links": "^3.4.2",
    "@storybook/angular": "^3.4.2",
    "@types/jasmine": "~2.8.3",
    "@types/jasminewd2": "~2.0.2",
    "@types/node": "^6.0.103",
    "babel-core": "^6.26.0",
    "codelyzer": "^4.2.1",
    "jasmine-core": "~2.8.0",
    "jasmine-spec-reporter": "~4.2.1",
    "karma": "~2.0.0",
    "karma-chrome-launcher": "~2.2.0",
    "karma-coverage-istanbul-reporter": "^1.4.2",
    "karma-jasmine": "~1.1.0",
    "karma-jasmine-html-reporter": "^0.2.2",
    "protractor": "~5.1.2",
    "ts-node": "~4.1.0",
    "tslint": "~5.9.1",
    "typescript": "~2.5.3"
  }
}

Compodoc installed globally or locally ?

Locally

Motivation for or Use Case

The navigation is not usable.

Reproduce the error

1. Remove the documentation folder

rm -rf documentation/

2. Run the compodoc watch command

npm run compodoc:watch

3. Load the page with a component http://127.0.0.1:8080/components/MyComponent.html
   Navigation OK.

4. Change the file my.component.ts

5. Watch is running

6. Load the page with the same component http://127.0.0.1:8080/components/MyComponent.html
   Navigation is broken.

Error:

before and after

<ul class="links collapse in" id="modules-links" aria-expanded="true" style="">
<ul class="links collapse" id="modules-links">

<a href="../components/MyComponent.html" data-type="entity-link" data-context="sub-entity" data-context-id="modules" class="active">MyComponent</a>
<a href="../../../components/MyComponent.html" data-type="entity-link" data-context="sub-entity" data-context-id="modules">MyComponent</a>

Compare both results with git

[lock]

This issue has been automatically locked due to inactivity. Please file a new issue if you are encountering a similar or related problem. Why locking ? Having issues with the most up-to-date context.