Xcode pbxproj file's structure got changed

Question

For some reason - maybe has to do with a latest Xcode upgrade to version 7.2.1 - my pbxproj's structure got changed, and because of that, when I'm about to merge a PR, it just shows me a one big conflict on the entire file.

The reason, as I see it, is that one of them has this structure (posting the start of the file):

// !$*UTF8*$!
{
    archiveVersion = 1;
    classes = {
    };
    objectVersion = 46;
    objects = {

/* Begin PBXBuildFile section */
        009025BEF30C41848E6869F6 /* RolloutDynamic_18.m in Sources */ = {isa = PBXBuildFile; fileRef = E1BF845EAB9E4962853253B5 /* RolloutDynamic_18.m */; settings = {COMPILER_FLAGS = "-fobjc-arc"; }; };
        00AFDB74BD584F1C9BD41B9D /* RolloutDynamic_03.m in Sources */ = {isa = PBXBuildFile; fileRef = 588F21D12977444EAE3C70F5 /* RolloutDynamic_03.m */; settings = {COMPILER_FLAGS = "-fobjc-arc"; }; };
        054D17D506BF45EE98822AB9 /* RolloutDynamic_15.m in Sources */ = {isa = PBXBuildFile; fileRef = 54D47CE8182E4482955DA02E /* RolloutDynamic_15.m */; settings = {COMPILER_FLAGS = "-fobjc-arc"; }; };

and the other one that structure (start of the file):

 <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>archiveVersion</key>
    <string>1</string>
    <key>classes</key>
    <dict/>
    <key>objectVersion</key>
    <string>46</string>
    <key>objects</key>
    <dict>
        <key>18011C201B1F865300F52714</key>
        <dict>
            <key>fileEncoding</key>
            <string>4</string>
            <key>isa</key>
            <string>PBXFileReference</string>
            <key>lastKnownFileType</key>
            <string>sourcecode.c.h</string>
            <key>path</key>
            <string>UserProfileTableViewController.h</string>
            <key>sourceTree</key>
            <string>&lt;group&gt;</string>
        </dict>

Any idea how can this be solved?