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Can't find rules on how commas work with relative clauses.

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すると石の下から斜{はす}に自分の方へ向いて青い茎{くき}が伸びて来た。見る間に長くなってちょうど自分の胸のあたりまで来て留まった。と思うと、すらりと揺{ゆら}ぐ茎{くき}の頂{いただき}に、心持首を傾{かたぶ}けていた細長い一輪の蕾{つぼみ}が、ふっくらと弁{はなびら}を開いた。

Problematic part:

すらりと揺{ゆら}ぐ茎{くき}の頂{いただき}に、心持首を傾{かたぶ}けていた細長い一輪の蕾{つぼみ}が、ふっくらと弁{はなびら}を開いた。

My understanding of how grammar works here:

X頂にY蕾がA

X and Y are both relative clauses that describe (respectively) the tip and the bud. に marks location (the stem's tip), が the active agent (the bud), Y the active agent's action (lit. "luxuriantly opening petals") that happens in the place marked by に、 (the stem's tip).

Is this the right way to think about it?

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I must say that your understanding of the sentence is 100% accurate.

Rules regarding the use of commas around relative clauses (or anywhere for that matter) in Japanese are not nearly as strict as in English. Where to use commas is pretty much left at the discretion of each writer.

The two commas used in 「すらりと揺ぐ茎の頂に、心持首を傾けていた細長い一輪の蕾が、ふっくらと弁を開いた。」 seem more than reasonable to me. They surely help the readers understand the exact structure of the sentence.

Had the sentence been written in the structure "subject + location + action", it might well have used only one comma as in 「心持首を傾けていた細長い一輪の蕾が、すらりと揺ぐ茎の頂にふっくらと弁を開いた。」 even though that still would be the author's choice instead of ours.

The comma after 「蕾が」 would not be omitted by almost anyone because the phrase modifying 「蕾」 is fairly long to begin with.

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