Just happened to notice this thread, and had been poking my own tileset a bit a couple weeks ago so it wouldn't need modbase to be installed (though I haven't really played DF recently) and thought I'd make some comments.
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This post is mainly for RantingRodent, but others may find something of interest here too.
*casts WALL OF TEXT*
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First, it looks like you've done quite a nice job, but there are a few things I'd like to give a bit of advice about (whether you consider it important or not is your decision, of course), mainly things that I either tried and discarded, or suggest deliberately chose to do in my tileset.
1. Anthills and bracelets are far more common than wells, all three use the same tile, none of them can be changed, and you've used a detailed picture of a well. I tried the same thing originally. It looks very bizarre in the middle of an ant-infested desert. I chose to use a generic circle-ish picture, personally.
2. At least here, the green (in-game) trees all have trunks that are much much darker than the trees - so much so that they're almost invisible here (I don't expect they are for everyone else, since I have my display gamma and such set up far darker than most people do, however).
I found a way to cheat on this, though, and you could probably do the same. When I made art for the feather tree, I gave it a brown background color in the raw file, painted the actual background black, and painted the tree's trunk the background's magenta color so that it would show up as brown all the time. I don't know if that would screw with crafting, but you've got craft_color figured out, yes? So that shouldn't be a problem?
3. Dark stone doors seem to be extremely difficult to see - they're really dark.
4. There was a reason there was transparency in the door art in my set other than just in the corners - so that the secondary door color, which was the only place you get the red of bauxite, green from olivine, yellow from orthoclase, etc, would show up in the door proper. You've got the entire door turned solid grey/black.
5. The overland rivers looking like they were made of bricks was unacceptable to me, and rough stone walls looking like they were made of bricks also unacceptable, and wooden bridges looking like they were made of bricks as well. This is why I would advise not using brick wall art, and is why I used something something more akin to a solid rough wall in my set instead.
6. Using colors in the font tends to be a bad idea*. Take your levers for instance. If someone builds a white lever, yay it'll look normal. If someone builds a bauxite lever, it'll probably look red when off and black when on. If they build an olivine lever, it'll probably look black when off and green when on. And if they build some kind of blue lever (or a dark stone one!) by chance, it'll probably look black whether it's on or off...
That would be why I wrote text instead of using color. That and the disappearing tree trunks are also why I ended up making tree trunks non-specially-shaded by default in mine.
* The glumprong, feather tree, and tower cap were exceptions, since the glumprong and tower cap were both seasonless and thus always one color, and I cheated on the feather tree like I mentioned before to give it a brown trunk regardless of coloring.
7. About stone colors being broken, the only one that was odd in mine was granite, and that was because the fg/bg reversal screwed up so many images which wouldn't have been a problem with ASCII. I changed it to 7:7:0, which is light grey on light grey. To quote my dev notes: "That might seem odd, but it keeps its stuff light grey while making its doors not be reversed - actually, its doors look like chalk/limestone/etc doors, but that's better than looking bizarre. However some granite items may look odd, particularly hatches. (It looks like there might be another way to do this, though. Some stone types have a [BASIC_COLOR:7:0] component - maybe that would make items made from it light grey on black)"
Your problem is probably that in many of your images, you've gotten rid of the transparency (or used images that did that) - which is really the secondary color, or in some cases the primary (example: wooden cages, and bins) - and replaced it with more greyscale or black. The solution is to do either what you did with the stairs, or shading with a technique like dithering, like I did on the barrel before and on the hatch in mine. You can also see how I did the door in mine. Also note why the bin in Sphr's had two box outlines but wasn't filled in (unless he changed that after I copied the image into mine).
I don't think I knew about the build_color keyword, it sounds like that does what I thought basic_color might do (I think I tried basic_color to no avail a week or so after writing that).
8. As for the graphics set, I see some things that are better than the one I'm using (veryinky's dystopian qantas set), notably that military units have multiple colors which are very distinct, and very big weapons, but on the whole it seems more difficult to tell what anyone is. Replacing the graphics set is easy as pie, though.
9. Overriding both [ and ] is a very good idea and I wonder why nobody before you thought of that.
Nice job improving the barrels, although it took me quite a while to get them to where I was satisfied with them originally, now that you've redone them the only problem is that it looks like they've got no bottom
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P.S. Did you know about the tower-cap art I made? You still seem to be using 0x06 for tower-caps. The art I made is at 0xac in my font if you want to use it - looks like a purple mushroom with a brown woody stalk. You also have glumprongs and feather trees using one image still - I had separate art for glumprongs at 0xab (It looks like a blue double-decker mushroom and has red glowy eyes around it) and feather trees at 0xf5 (It's green, surrounded by black, and has two transparent-color trunks). Maybe you already knew about them and chose not to use them, or maybe you didn't know what they were for because you didn't know that I wrote down the changes I made in a log file that I included with the tileset.
Edit again:
I figured I should show those. Screenshots (using my tileset with the natural color scheme, or whatever slight modifications to it I had made):
glumprongs:
http://screencast.com/t/jcjtkoh5Lfeather trees:
http://screencast.com/t/9YAgdF3Ztower cap:
http://screencast.com/t/oyp0kCRn - this one isn't a screenshot, it's just from the font with the background turned black, since I haven't found any underground water sources in any of my forts in any 3d versions.