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Some online dictionaries list the shorter writing as "irregular". What does this mean exactly? Were those words used like that long ago? Is it an abbreviation with writing? Or a slang?

Note that I'm not asking for an explanation of the difference between 上【のぼ】る and 上【あ】がる.

Not sure how to tag this because I have no idea why this is happening.

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The official jōyō kanji chart lists 上{あ}がる and 明{あか}るい. It does not list 上{あが}る and 明{あかる}い. In other words, the latter two are not official ways to write these words.

Of course, people don't always follow the official recommendations, and even today you'll find some variation in how people use okurigana, but I think you'll find in this case that the official way is much more common.

So why are they included in the dictionary? According to Jim Breen's EDICT documentation (and I assume you're using EDICT because it's the only dictionary I'm aware of that has an "irregular okurigana usage" tag), variants are included "to enable software to match with variant forms". For the most part, you can ignore these―you'll come across variations in okurigana yourself from time to time, but it's usually obvious how to read them in context, and the two you picked out aren't especially common.

You can read more official recommendations for okurigana usage on the Agency for Cultural Affairs website, although actual usage doesn't always follow these recommendations.

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