File: src/java/org/apache/commons/cli/HelpFormatter.java
Issue: HelpFormatter wraps incorrectly on every line beyond the first
The method findWrapPos(...) in the HelpFormatter is a couple of bugs in the way that it deals with the "startPos" variable.  This causes it to format every line beyond the first line by "startPos" to many characters, beyond the specified width.  
To see this, create an option with a long description, and then use the help formatter to print it.  The first line will be the correct length.  The 2nd, 3rd, etc lines will all be too long.
I don't have a patch (sorry) - but here is a corrected version of the method.
I fixed it in two places - both were using "width + startPos" when they should have been using width.

 protected int findWrapPos(String text, int width, int startPos)
    {
        int pos = -1;

        // the line ends before the max wrap pos or a new line char found
        if (((pos = text.indexOf('\n', startPos)) != -1 && pos <= width)
            || ((pos = text.indexOf('\t', startPos)) != -1 && pos <= width))
        {
            return pos+1;
        }
        else if ((width) >= text.length())
        {
            return -1;
        }

        // look for the last whitespace character before startPos+width
        pos = width;

        char c;

        while ((pos >= startPos) && ((c = text.charAt(pos)) != ' ')
               && (c != '\n') && (c != '\r'))
        {
            --pos;
        }

        // if we found it - just return
        if (pos > startPos)
        {
            return pos;
        }

        // must look for the first whitespace chearacter after startPos 
        // + width
        pos = startPos + width;

        while ((pos <= text.length()) && ((c = text.charAt(pos)) != ' ')
               && (c != '\n') && (c != '\r'))
        {
            ++pos;
        }

        return (pos == text.length())        ? (-1) : pos;
    }

Buggy code:
protected StringBuffer renderWrappedText(StringBuffer sb, int width, 
                                         int nextLineTabStop, String text)
{
    int pos = findWrapPos(text, width, 0);

    if (pos == -1)
    {
        sb.append(rtrim(text));

        return sb;
    }
    sb.append(rtrim(text.substring(0, pos))).append(defaultNewLine);

    // all following lines must be padded with nextLineTabStop space 
    // characters
    final String padding = createPadding(nextLineTabStop);

    while (true)
    {
        text = padding + text.substring(pos).trim();
        pos = findWrapPos(text, width, nextLineTabStop);

        if (pos == -1)
        {
            sb.append(text);

            return sb;
        }

        sb.append(rtrim(text.substring(0, pos))).append(defaultNewLine);
    }
}

Fixed code:
protected StringBuffer renderWrappedText(StringBuffer sb, int width, 
                                         int nextLineTabStop, String text)
{
    int pos = findWrapPos(text, width, 0);

    if (pos == -1)
    {
        sb.append(rtrim(text));

        return sb;
    }
    sb.append(rtrim(text.substring(0, pos))).append(defaultNewLine);

    // all following lines must be padded with nextLineTabStop space 
    // characters
    final String padding = createPadding(nextLineTabStop);

    while (true)
    {
        text = padding + text.substring(pos).trim();
        pos = findWrapPos(text, width, 0);

        if (pos == -1)
        {
            sb.append(text);

            return sb;
        }

        sb.append(rtrim(text.substring(0, pos))).append(defaultNewLine);
    }
}