<p dir="auto">Hi, and first, thank you so much for your project.</p>
<p dir="auto">This problem first appeared in my work project which is unfortunately private. All my files was considered as ignore and appeared in grey in the treeview. I took some time and finally succeed to isolate and reproduce it.</p>
<p dir="auto">In a Git project, if a .gitignore from a subdirectory match a path from the root of the project, the treeview will use the rule and ignore the path while it's incorrect. Indeed, Git will not do the same mistake and the <code class="notranslate">git status</code> will be different as what Atom show.</p>
<p dir="auto">You can easily test on this repository I create to demonstrate the problem:<br>
<a href="https://github.com/Swiip/atom-git-tree-test">https://github.com/Swiip/atom-git-tree-test</a><br>
The <code class="notranslate">test.txt</code> file inside the src directory should not be displayed grey as it's not ignored in git.</p>
<p dir="auto">If it's needed, I tested on a Mac with OSX 10.9.5, Atom 0.134.0, I tried several times to delete cached files and it change nothing. I have no error in the developer panel.</p>
<p dir="auto">I've the following setup:</p>
<div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="&gt; tree
.
└── ipfs
    ├── .gitignore
    ├── ipfs
    ...
&gt; cat ipfs/.gitignore
ipfs

&gt; echo because ipfs/ipfs is a binary.
and atom is ignoring the entire ipfs/ directory

&gt; echo this shouldnt happen because the .gitignore
is within the directory, and shouldn't apply outside!"><pre class="notranslate"><code class="notranslate">&gt; tree
.
└── ipfs
    ├── .gitignore
    ├── ipfs
    ...
&gt; cat ipfs/.gitignore
ipfs

&gt; echo because ipfs/ipfs is a binary.
and atom is ignoring the entire ipfs/ directory

&gt; echo this shouldnt happen because the .gitignore
is within the directory, and shouldn't apply outside!
</code></pre></div>
<p dir="auto">thanks all ❤️</p>
<p dir="auto">(Stopgap: do <code class="notranslate">./ipfs</code> in .gitignore. but this shouldn't be necessary).</p>