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So the background on my plugin - it generates taxonomy/term filters to give you a filtering system similar to what you'd see on NewEgg where you filter your results by category/manufacturer/other criteria.

In the admin area, users will create a filter-set. The filter-set will have various options (display name, type, etc). Within the filter set are the individual taxonomies that the filter-set will be made up of. These can be re-ordered using drag and drop (their order needs to be stored since they will need to be displayed in that order). Each of the taxonomies also has various options like display name, menu type (drop down, radio button, multi select, etc) and various other options.

Ultimately it will look something like this (the ordering of the 'taxonomy' nodes must be retained);

<Filterset-01 option1="" option2="">
  <taxonomy tax="c"  option1="" option2="" option3="" />
  <taxonomy tax="b"  option1="" option2="" option3="" />
  <taxonomy tax="a"  option1="" option2="" option3="" />
</filterset-01>

<Filterset-02 option1="" option2="">
  <taxonomy tax="d"  option1="" option2="" option3="" />
  <taxonomy tax="a" option1="" option2="" option3="" />
  <taxonomy tax="e" option1="" option2="" option3="" />
</filterset-02>

So far I set up my own db table but I feel like this might not be the best method. I can probably store the whole thing in a big, complicated array and just save it a single option in wp_options but I don't know if that's a good idea. I was also considering XML since I already visualize the plugin structure in pseudo XML but I don't know if there is any preferred method for storing options in XML or what drawbacks it may have.

Basically I just want to know what the ideal method for storing the above data would be.

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1  
are you just loading all the data in one go, or do you need to query on any of the data contained within? –  Milo Mar 11 at 0:26
    
All the data within a given filter-set will be loaded. The user will use a shortcode to call a specific filter-set and then that filter will be generated based on the stored ordering and options. –  George Kendros Mar 11 at 0:46
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