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Markdown allows underlining or # titles, this seems to ignore the underlined ones:

# Header 1

Header 1
--------

## Header 2

Header 2
=======

If any headers have code tags in them, the automatically generated hyperlinks don't work. To fix this, simply remove any backticks (`) from the links.

An example with broken links due to backticks in links:
https://github.com/rbotts/Occupancy/blob/446c2205c8c78eddc87ebd20a86e1bad850dfdea/UnmarkedGuide.md
(note that the two TOC items without any code tags have working links, but all the TOC items with code tags, such as "Creating colext models" do not have working links.)

An example with those links fixed by removing the backticks:
https://github.com/rbotts/Occupancy/blob/f134cb8cb9626463e71df73c01681112eb004e9b/UnmarkedGuide.md
(note that now even the TOC items with code tags do have working links.

The diff between the two:
rbotts/Occupancy@f134cb8#diff-776f5c8d16bf7b01e8f44ec08d2ac678

When using pandoc to generate html output, md-to-toc fails to match the generated id if the heading contains a full stop or more than one consecutive space:

Source markdown:

# Multiple   spaces.

Pandoc output:

<h1 id="multiple-spaces.">Multiple spaces.</h1>

md-to-toc output:

- [Multiple   spaces.](#multiple---spaces)

Pandoc keeps the full stop while md-to-toc strips it out.

Pandoc collapses multiple spaces into a single dash while md-to-toc converts every space to a dash.

md-to-toc is designed to replicate GitHub's algorithm for determining anchor strings and GitHub may well handle these cases differently to pandoc. Thought I'd bring it to your attention anyway.

Aside from these two issues, which were trivial to work around, the script worked very well and saved me a lot of time. Thanks!