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When I go into the Market app and into my downloads list I can see that 5 of my apps have an available update.

Three of the apps say "Update" in orange, and two of them say "Update (manual)" in dark red. If I click through to the app I just get the normal "Update" button for both the "manual" and otherwise ones.

I assume this is something new with the Froyo version of the Market, but can't work out what the difference is?

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You will see Update (Manual) when the app's permissions have changed. So during the Manual update, you should be asked whether you accept the new permissions. Here's a reference from the Android Market forum. I read this somewhere else but this seems to be the only place I can find it right now. Quoting the link:

Froyo added an auto-update feature for your apps. If an app has an update and no new permissions, it will be marked as the orange "update." If an app has changed its permissions, then it's red and you need to manually update it (after checking and verifying the new permissions of course).

...

One more thing, you can verify this when you update your apps. If the app was a normal "orange" update, when you click update, it will start downloading right away. If the app was a manual "red' update, when you click update, you have to agree to the new permissions, then it starts downloading.

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Ahhh, so "Manual" just means the update works the same way they all used to pre-Froyo. Nothing scary at all (assuming the permission change isn't outrageous). –  GAThrawn Nov 18 '10 at 17:39
    
Yeah, for example, Google Sky Map has Update (manual) on my phone right now. After I select Update > OK. It lists the permissions: the app has access to Your Location (fine GPS access), Network Communication (full internet access) and System Tools (modify global system settings, prevent phone from sleeping). I can't figure out which features in the app require use of the Internet but the other two updates are OK with me. –  gary Nov 18 '10 at 17:56
    
@GaThrawn Correct. Manual is just throwing a red flag at you saying "Hey! Some permissions have changed! Look at them before you upgrade me!" –  Bryan Denny Nov 19 '10 at 14:38
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