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For the quality & efficiency, editing should better to do following order.

1) rotate/merge/crop
2) filter
3) mask/clone/patch
4) redraw details in gaps which original image hasn't

It's a pain when I edit only one image to switch applications. but when I use batching on 2), there are no painful switching because process 1) & 3) are separated.

I use SAI only on 4). but I haven't filled gaps recently, so don't been used SAI several weeks :P

File format: 1):bmp result of 2)&3):psd.

Use only psd on PS because Adobe hates to write other formats. I'm using Xnview to export psd into others.