Haglund's deformity is a common problem for runners; if you've never heard of it, you probably don't have it (it's genetic). I've run more than 80,000 miles with an advanced case of it and I think the medical advice available on the web only makes sense if you've just found a pea-to-marble sized bump on your heel, not if you've had it for a long time and your heels look like mine:
Here's the common advice and my take on it:
1) Take anti-inflammatories.
If you've had the problem for more than 6 months, it's no longer an inflammatory response and you've progressed from tendinitis to tendinosus. Taking painkillers may cause you to run on an injury when you shouldn't.
2) Use heel lifts.
The idea is that raising the heel may change the angle between the calcaneus and tendon and avoid the two rubbing against each other. Heel lifts decrease the range of motion of the ankle and thus limit the speed with which one can run; it also causes the tendon and calf muscles to shorten, which exacerbates the problem.
3) Don't run hills.
If running up a hill hurts, try modifying your stride or slowing down. If there's no way to eliminate the pain, then avoid that hill if possible, but continue to run the hills you can do without pain.
4) Wear orthotics.
The idea is that pronation causes the tendon to rub in a twisting fashion against the deformity in the heel, but there has never been evidence that orthotics help that's been published in the scientific literature.
5-7) Always wear new shoes, cut a notch in the material over the bump, wear padded socks or padding with a hole at the bump.
My heels always hurt more with new shoes and running in them causes the material to wear out over the bump, making them more comfortable. Padding just decreases the space in the shoe, making rubbing problems worse.
8) Wear minimalist shoes or go barefoot.
Most minimalist shoes hold tightly against the heel, which is a problem. If you can run comfortably in huaraches, they would be a good choice; here in Minnesota, there's something we call winter, which makes them impossible. When not running, go barefoot or wear flip-flops as much as possible.
What Actually Works
Surgery is the common option. After 30 years, I may have mine this year.
If surgery's not an option, then there's three things to consider: tendinosus, retrocalcaneal bursitis and sequelae (the things that go wrong because you've changed your running style to minimize pain).
There are two treatments for achilles tendinosus that claim to have 100% success rates and which have helped me: stretching under eccentric load and self-myofascial release.
Stretching the Achilles and calf
The common stretches for the gastrocnemius and soleus muscles - the wall stretches - aren't enough. The proper stretch is done as follows: Find a stairwell, preferably where you can touch walls on either side of the steps, for support when needed. Place one foot on the edge of a step, the other foot held behind the line of the body. Raise onto your toes and lower yourself slowly (about 2 seconds) as far as possible. Then bend the knee of the leg being stretched as much as possible. Raise up again, using your arms and other leg if needed. Do three sets of 15 stretches with each leg, twice a day.
When I first started, I could only do these doing both feet at once. Within a month, there was considerable improvement.
Deep tissue massage, active release therapy, whatever you call it, breaking the adhesions on the tendon manually will allow the tendon to heal normally. Start by using a foam roller (there's a ton of videos out there showing how to do this) over the entire length of the tendon. Then press into the tendon with your thumbs at any point that's painful, as hard as possible (you can actually sprain your thumbs if you're not careful). Pinch the cord between thumb and forefinger and rub both side-to-side and up-and-down. To create greater pressure and save your fingers, use a golf ball pressed into the tendon with your palm and roll it over the area. Massage for 15 minutes per day per leg.
The golf ball thing was my idea. At first, the area of attachment at the base of the tendon was excruciating to press on this way and I actually cried while doing it, but within a month it no longer hurt there. The area where the bursae have pushed out laterally from the tendon has been more difficult to treat, but improved over 6 weeks. The area directly over the bump was never the biggest problem for me, but has been slow to improve. Lastly, there have been occasional flare-ups at the narrowest point of the tendon (actual tendinitis!), which improved in a day or two with careful management.
All the other stuff
When you run, you'll naturally find what causes the least amount of pain. This won't be the most efficient way to run and you'll be forcing parts of your body to take up more of the load than they're designed for, so you'll likely develop problems in other areas. You should do a range of maintenance exercises to protect against: plantar fasciitis, shin splints, peroneal tendinitis, tarsal tendinitis, hamstring tendinitis, iliotibial band syndrome, piriformis syndrome and quadriceps and hip adductor strains. Really - I've had all of them and more.
That's a lot of work to do on top of running and even that seems to be failing me after 30 years. That's why I'm looking at surgery as a last resort.