I completed my MA in 2014 (humanities, third world country) but due to very bad (almost non-existent) supervision and other reasons my thesis is subpar in some areas (e.g., research design, data analysis). However, during the past 7 years I have not only been working in my field, but I have also managed to make up for this by publishing a couple of world class peer-reviewed articles, have a couple of articles under review in flagship journals, and a book chapter with a quality publisher to be released soon. Now, I am applying for a PhD and they want my MA thesis among other documents. It does not reflect my "current" research abilities at all so I think it is not a fair way to assess me now after all this time, effort, and achievement.
In any case, how can I confront this situation? I was thinking about adding a cover letter to my thesis which indicates upfront that this thesis is not my best work and may have flaws and then proceeding to more precisely refer to these flaws and how they can be rectified.
Is this a good strategy? Do you have any other suggestions?