Here's the updated ARD Tagesschau story, translated as before by yours truly:

The Munich State prosecutor (Part I) has secured arrest warrants for 13 accused CIA Agents.  The agents will face charges of having abused and kidnapped the German Khaled al Masri in January 2004.  Al Masri was taken into custody under suspicion of terrorism in Macedonia and then dragged off the Afghanistan.  After four months in a CIA secret prison he was freed.  Officially, the US is silent on the case, though unofficially many on the US side have conceded that Masri was seized by mistake.  

The 13 agents of the US-secret service (CIA) now being sought under the arrest warrants are being held responsible for flying al Masri from Macedonia to Afghanistan on January 23, 2004 on a Boeing 737.  It was not only the Munich State prosecutor which has come to be on the trail of the eleven men and two women. ZDF*-research had revealed that the kidnap aircraft bearing the tail number N313P flew from Mallorca to the Macedonian capital Skopje.  

In the course of their investigation the Spanish police discovered that the aircraft's mission was staged from the Balaeric island's Hotel Mariott Son Antem and found the names and passport numbers [of the perpetrators] there.  The thirteen names were all cover identities.  The ARD magazine show Panorama was able, in the past autumn, to uncover some of the CIA agents and seek them out in their private residences in the US state North Carolina.

The Prosecutor's office tries with Cover Names

The arrest warrants from the Munich state prosecutor (part I) are not made out in the already-researched true names of the agents, but rather under their cover names.  The State prosecutor continued, that the further analysis will now concentrate on investigation of the true identities.  Therefore, the arrest warrants presently being sent out are only an intermediate goal/step.  It is certain that the USA will not turn over their secret-service agents.  There also remains the chance that the 13 being sought will be picked up on their arrival in Europe.  But it is also unlikely that, if one of the agents should travel to this side of the Atlantic in the face of the German arrest warrants, they would travel under the already-disclosed (and shown as false) cover names.  

Lawyer:  the arrest warrants are ,,clarifying act"

Notwithstanding all this, the lawyer for al Masri, Manfred Gnjidic, says the arrest warrants are a step in the right direction.  It is the first time in the entire case, says Gnjidic to Tagesschau.de, that German authorities have gone against the US side's story.  With this "clarifying act" the prosecutor's office has made clear that the CIA in foreign countries cannot simply do as it pleases and how it pleases.  That (doing as it pleases and how it pleases) has been the nourishing center of the US tactics in the War against Terror, added Gnjidic.

There are also Italian arrest warrants against CIA Agents.

The German arrest warrants are not this first issued from European courts in connection with the CIA kidnappings.  In a similar case Italian investigators have issued arrest warrants against 26 CIA agents and five Italians.  These accused are alleged to have responsibility for taking part in the kidnapping of the Islamist Abu Omuar.  In February 2003, Omar was jerked into a car in Milan in broad daylight, brought the US Air Force base Aviano and from there, through the US base at Ramstein Germany, flown on to Egypt.

Pressure on the transatlantic relationship?

The investigations of the Italian prosecutors have unleashed possibilities that could adversely affect the relationship between Rome and Washington.  Actually, the course of the investigation was such that the Chief of the CIA detachment in Milan, Robert Seldon Lady, left Italy in a hurry.  After he failed to appear before a preliminary proceeding (sort of an investigative hearing) before an Italian Court at the beginning of January, the authorities permitted a search of Lady's villa in Piedmont.  Also, the cooperation between the Italian military intelligence SISMI and the US services has been disturbed.  (N.B.  there have long been allegations SISMI was the source, or close to it, for the Niger Uranium forgeries, so I can't see how this would make things worse, assuming they are actually worse.)  The former head of SISMI, Nicolo Pollari, has been brought before the Court because of the Omar kidnapping.  Because Pollari will not allow himself to be made a scapegoat, he has already made clear his intention to share his knowledge (with the investigation).

The consequences of the German arrest warrants against the responsible CIA-agents is presently unclear.  Following upon the prosecutor's office, the Bundesnachtrichtendienst (their intelligence service) put the al-Masri kidnapping "under the loupe".  But thus far carrying out a proceeding on Germany's part carrying a real risk of criminal penalties is something which has not been proven certain. (i.e., I understand this to meand it's not yet clear whether the prosecutor will be able to see this through.)  Thus far in Germany a criminal proceeding such as against Pollari in Italy has been foreclosed/thwarted.

The Foreign Ministry diplomatically holds itself back.

Whether this will place an additional strain upon German-American relations is still to be seen.  The Foreign Ministry refused to take a position in response to Tagesschau.de.  Instead, the Ministry said prosecutorial investigations and their results are to be independent of politics.

- -
My analysis of the seeming incongruity - that this story indicates the warrants were issued in the cover names while ARD has already been able to find the true identities of the agents and seek to interview them admits of at least two possibilities.  (A) there's a techinical legal problem with issuing a warrant in the real name - like either a lack of connective proof sufficient legally to support a warrant, or a requirement that when a false name is used, that the warrant be issued against the false name with an "a/k/a".  Or (B), political or legal considerations require them to issue the warrants in the false names.

More importantly is the characterization of this as a "clarifying act".  I read this as a sort of "which side are you on" moment.  On the one hand, they can be tools of the Global Wah on Terrah and just look past this.  On the other, they can apply the lessons learned from their own history and require all legal and moral proprieties be observed.  I think this is another little snowball at the top of the hill.  It was heartening to see them issue the warrants.

As the Times article notes:

"This is a very consequential step," August Stern, the deputy prosecutor in Munich, said in a telephone interview. "It is a necessary step before bringing a criminal case against these people."

why? simply put, germany needs us, and our intelligence services. there is a long standing history of cooperation between the cia and german (west) intelligence agencies. they aren't going to let a minor matter like this get in the way.

Seems former Italian intelligence (SISMI) head, Nicolo Pollari is gonna have to face indictment on role in helping the Bush administration's (intelligence laundry business) kidnapping and rendition project.

 Prosecutors want to try 26 Americans, most believed to be CIA agents, for grabbing Muslim cleric Hassan Mustafa Osama Nasr off a Milan street in 2003 and flying him to Egypt, where he says he was tortured.

Italy's former spy chief Nicolo Pollari, who risks indictment on suspicion of aiding the CIA mission, wanted Prodi and Berlusconi to defend him at a preliminary hearing since he says information proving his innocence is classified.

<snip>

If she orders a trial, as looks increasingly likely after Tuesday's ruling, it would be the first criminal procedure over renditions -- one of the most controversial aspects of U.S. President George W. Bush's global war on terrorism."

The case is being closely watched all over Europe, where judicial authorities in several countries are investigating accusations of CIA secret prisons and secret transfers of U.S. terrorism suspects.

Yep, our ally in the war on terror - Italy, wants to try 26 Americans on charges of kidnapping, while in Germany, a judge ordered that 13 Americans be arrested. So that now makes 39 people (assuming there are no overlaps) who either "pretended" to be CIA or are CIA and were acting on direct orders of Bush administration officials.