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D (419 chars)

enum c=q{string[string] m;import std.stdio;import std.array;void main(){foreach(string s;lines(stdin)){auto a=s.split;if(!a.length)goto e;switch(a[0]){case "*":m.clear;break;case "!":m.remove(a[1]);break;case "?":writeln(m.get(a[1],""));break;default:if(a.length<2){goto e;}m[a[0]]=a[1];}stdout.flush;}e:write("static this(){");foreach(i,v;m)writef("m[`%s`]=`%s`;",i,v);write("}enum c=q{",c,"};mixin(c);");}};mixin(c);

formatted:

enum c=q{
    string[string] m;
    import std.stdio;
    import std.array;
    void main(){
        foreach(string s;lines(stdin)){
            auto a=s.split;
            if(!a.length)goto e;
            switch(a[0]){
                case "*":m.clear;break;
                case "!":m.remove(a[1]);break;
                case "?":writeln(m.get(a[1],""));break;
                default:if(a.length<2){goto e;}m[a[0]]=a[1];
            }
            stdout.flush;
        }
        e:write("static this(){");
        foreach(i,v;m)writef("m[`%s`]=`%s`;",i,v);
        write("}enum c=q{",c,"};mixin(c);");
    }
};mixin(c);

variant of my D quine

the * command relies on m.clear; to work correctly which it doesn't in dmd 2.52 (bug in the compiler)

the need for stdout.flush; depends whether auto flush is enabled (it isn't on my machine)