How to update GitHub porfolio when there are multiple file types .md .html .rmd files?

While ago I had created github.io portfolio for my teaching class.

Now I want to update it by adding additional navigation to provide resources to students.

I am able to link dropdown navigating .HTML files to navigating HTML files. However, once the page moves to a new HTML file, it doesn't show newly created navigated files on the top.

e.g.

<div class="navbar navbar-default  navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <a class="navbar-brand" href="index.html">My Name</a>
    </div>
    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav">
        <li>
  <a href="index.html">Home</a>
</li>
<li>
  <a href="Biology-101.html">Biology 101</a>
</li>
<li>
  <a href="Biology-115.html">Biology 115</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
    Home Work
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="Week-1.html">Week-1 (Fall 2021)</a>
    </li>
     <li>
      <a href="Week-2.html">Week-2 (Fall 2021)</a>
    </li>

Do I have to add new codes (created for new files) to every other manually— i.e. readme.html index.html Biology-101.html Biology-101.html etc.?

For example, here is a screenshot of the types of some files I have on GH.

May I know what is the difference between readme.html and index.html files? Also, I have no idea how these .MD .RMD files were generated.

I would be really grateful if anyone could help me to understand how to update the codes.