(Unity Xcode Manipulation API) An example which modifies compiler flags for a given source file.

PbxModifier.cs

using UnityEngine;
using UnityEditor;
using UnityEditor.Callbacks;
using UnityEditor.iOS.Xcode;
using System.IO;

public class PbxModifier
{
    [PostProcessBuild]
    public static void OnPostprocessBuild(BuildTarget buildTarget, string path)
    {
        if (buildTarget == BuildTarget.iOS) {
            string projPath = path + "/Unity-iPhone.xcodeproj/project.pbxproj";

            PBXProject proj = new PBXProject();
            proj.ReadFromString(File.ReadAllText(projPath));

            string target = proj.TargetGuidByName("Unity-iPhone");
            string file = proj.FindFileGuidByProjectPath("Classes/UnityAppController.mm");

            var flags = proj.GetCompileFlagsForFile(target, file);
            flags.Add("-fno-objc-arc");
            proj.SetCompileFlagsForFile(target, file, flags);

            File.WriteAllText(projPath, proj.WriteToString());
        }
    }
}

PostBuildProcess.cs

// link form http://qiita.com/tkyaji/items/19dfff4afe228c7f34a1

using UnityEngine;
using UnityEditor;
using UnityEditor.Callbacks;
using UnityEditor.iOS.Xcode;
using System.Collections.Generic;
using System.Text;
using System.IO;

public class PostBuildProcess {

    [PostProcessBuild]
    public static void OnPostProcessBuild (BuildTarget buildTarget, string path) {
        if (buildTarget == BuildTarget.iOS) {
            processForiOS (path);
        }
    }


    private static void processForiOS (string path) {
        string projPath = path + "/Unity-iPhone.xcodeproj/project.pbxproj";

        PBXProject proj = new PBXProject ();
        proj.ReadFromString (File.ReadAllText (projPath));

        string target = proj.TargetGuidByName ("Unity-iPhone");

        // tbd追加
        string tbdName = "libsqlite3.tbd";
        proj.AddFileToBuild(target, proj.AddFile("usr/lib/" + tbdName, "Frameworks/" + tbdName, PBXSourceTree.Sdk));
        // IOS9支持.tbd扩展名的库, Unity的PBXProject不支持将.tbd增加到 Link Binary With Libraaries
        // 需要手动支持Link Binary With Libraaries
        string projText = addTbdLibrary (target, proj.WriteToString (), tbdName);

        File.WriteAllText(projPath, projText);
    }


    // .pbxproj 修正 .tbd 库为 Link Binary With Libraries
    private static string addTbdLibrary(string target, string projText, string tbdName) {

        string[] lines = projText.Split ('\n');
        List<string> newLines = new List<string> ();

        string refId = null;
        bool editFinish = false;

        for (int i = 0; i < lines.Length; i++) {

            string line = lines [i];

            if (editFinish) {
                newLines.Add (line);

            } else if (line.IndexOf (tbdName) > -1) {
                if (refId == null && line.IndexOf ("PBXBuildFile") > -1) {
                    refId = line.Substring (0, line.IndexOf ("/*")).Trim ();
                } else if (line.IndexOf ("lastKnownFileType") > -1) {
                    line = line.Replace ("lastKnownFileType = file;", "lastKnownFileType = \"sourcecode.text-based-dylib-definition\";");
                }
                newLines.Add (line);

            } else if (line.IndexOf ("isa = PBXFrameworksBuildPhase;") > -1) {
                do {
                    newLines.Add (line);
                    line = lines [++i];
                } while (line.IndexOf("files = (") == -1);

                while (true) {
                    if (line.IndexOf (")") > -1) {
                        newLines.Add (refId + ",");
                        newLines.Add (line);
                        break;
                    } else if (line.IndexOf (refId) > -1) {
                        newLines.Add (line);
                        break;
                    } else {
                        newLines.Add (line);
                        line = lines [++i];
                    }
                }
                editFinish = true;

            } else {
                newLines.Add (line);
            }
        }

        return string.Join ("\n", newLines.ToArray ());
    }
}