Hi,
I have built protoc-gen-doc from source on OSX (10.11.6) (from master, commit 97718ab) following the given steps. HTML output seems correct but markdown output has a bug with mulit-line comments where the last word on one line is concatenated to the first word on the next line. Here is a minimal example:

test.proto

syntax = "proto3";

message Foo {
  /**
   * Some
   * long
   * description
   */
  bool bar = 1;
}

After running

protoc --doc_out=markdown,test.md:. test.proto

The file test.md is as follows - the important thing is the appearance of Somelongdescription with no spaces between the words.

# Protocol Documentation
<a name="top"/>

## Table of Contents
* [test.proto](#test.proto)
 * [Foo](#Foo)
* [Scalar Value Types](#scalar-value-types)

<a name="test.proto"/>
<p align="right"><a href="#top">Top</a></p>

## test.proto



<a name="Foo"/>
### Foo


| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| bar | [bool](#bool) | optional | Somelongdescription |

...