(By the way, spoilers through the sixth episode of series 6. Also, musing at length about things that you may not think need musing at length about. You are warned.)
If you watch Doctor Who closely, or spend a lot of time around the Doctor Who fan community, you probably became aware of the Eleventh Doctor's color-coded bow ties during series 5. While in the future, he wore a red bowtie, and in the past or present, he wore blue (with the exception of the first episode and the final 2-parter, when he does wear red despite being in the past and present).
He doesn't seem to be following that pattern this year. In "The Curse of the Black Spot" he wore red in the past, and in "The Rebel Flesh"/"The Almost People" he was wearing blue in the future. Maybe there's a new rule. Like, if Rory dies, the Doctor wears Red. Or something. He also seems to have a purple bowtie and suspenders in the first episode when he's Future Doctor. Or maybe it was just the light. I couldn't really tell.
Then there is a Doctor wardrobe plot point in "The Almost People," when the Doctor reveals that he and his doppelganger switched shoes so that everyone thought the doppelganger was the original.
Anyway, I'm not too interested in the Doctor's choice of clothing. No, this is going to center around the very plaid costume choices of one Amy Pond. First of all, to recap what she's worn so far this season:
Amy has two red plaid shirts, and she wears one or the other for at least part of every episode. Shirt Number One, which she wears for most of "The Impossible Astronaut" and all of "The Rebel Flesh"/"The Almost People" is a little more fitted, and is a brighter red with less white. Shirt Number Two, with a little more white in the plaid, was actually first seen before the season started, in the two part Red Nose Day special, and then is worn for a part of "Day of the Moon" and all of "Curse of the Black Spot" and "The Doctor's Wife." The only other tops we've seen Amy in are a darker purple plaid at the very beginning of the first episode, and the black suit in the second episode.
At this point, you may be wondering why I am so fixated on Amy's lack of clothing variation. She did, after all, start the season by packing a backpack and running off with Rory to meet the Doctor in Utah, hitchhiking on a school bus in the process. Maybe she just ended up packing one of her favorite flannels, and then wearing another, similar shirt, and didn't bring any of the solid-colored shirts that were her standard fare last season. She had at least a couple of pairs of boots and a couple of jackets in that bag, so there wasn't much room for anything else.
Therefore, while I am hesitant to dismiss anything as non-plot-important in Doctor Who, especially in the Moffat era of Doctor Who, I am willing to let one of these two shirts slide as just a shirt and not a plot point. That would be shirt number Two, the one she is wearing during the middle of the Spring run. At this point, I am willing to admit that it is only a shirt.
Shirt number One, however, does have some significant plot significance, as do the cropped skinny jeans that she wears with it.
Starting from about two minutes into "The Impossible Astronaut," Amy wears shirt number One, the cropped jeans, and brown sneakers. In one or two scenes she adds a tan jacket. She wears the same clothes through that episode, and is still wearing the same outfit at the beginning of the next episode until they all meet up and get back into the TARDIS, about six minutes in. Then in "The Rebel Fresh," she's wearing the same shirt and jeans, but this time with some tan ankle boots and a black leather jacket. Since, like most Doctor Who episodes, the entire two-parter takes place in the span of several hours, she's still wearing the same outfit through "The Rebel Flesh."
At the end of the episode, after everyone is seemingly out of danger and they're out of the cold, drafty monastery, Amy changes her outfit a bit- she is now wearing shirt number One, those cropped skinny jeans, no jacket, and brown sneakers instead of the boots she had on earlier. And that is what she is wearing when the Doctor reveals to her and Rory (and the audience, of course) that Amy isn't actually Amy, telling her, "You haven't been here for a long, long time," and sonic-ing her into a puddle of raw Flesh.
Okay. So why am I so fixated on what she was wearing at that point?
Well, it didn't specifically show every article of clothing she was wearing, but she had a perfectly duplicated outfit from the first episode at that point, and that from what we could see, her clothes went all Flesh with the rest of her. This indicates to me that she was wearing clothes that were made entirely of Flesh at that point- gangers can and do change clothes (especially since Amy didn't know she was one), but if she was wearing clothes that were the originals, she would have dissolved and left her clothing behind.
Gangers are created wearing whatever their original was wearing when he or she was scanned, so it seems to me that Amy must have been replaced while wearing that outfit- ergo, sometime during episode one or between episodes one and two. This is supported by the fact that she first sees eyepatch lady in the middle of episode two.
So there we go. My take on Amy's clothing in series 6 and it's significance. I kind of want to buy a red plaid shirt now.