I?m hoping to spark a general discussion over how people use Jaikoz. With the power and flexibility to adjust everything comes the daunting job of deciding on settings and optimizing workflow. I?ll say what I do and people can compare & contrast. I don?t expect one right answer will emerge, but I?m hoping it will be useful.
Note- I?ve been using Jaikoz for two years. I?m not an IT person or an engineer, so forgive the technical imprecision. I use iTunes on a Mac, so that?s my perspective. Lastly, I love this software and Paul?s attention to it.
Workflow
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Load files- loads about 3000 songs/minute. See separate post on Memory and Loading Files. 
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Retrieve acoustic ID- retrieves 6-10 PUIDs/minute. Worth retrying periodically as new PUIDs are added to the database and some PUIDs seem to missed in the first go-round. I have these save automatically by checking Save Acoustic IDs under Preferences-MusicBrainz-Music IP. 
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Manual correct tags from MB- try as I might, I can?t live with the results from Autocorrect tags?too many mismatched tracks. Manual correct takes lots of time but is still faster than undoing errors from a hasty Autocorrect & save. See separate posts on Manual vs. Autocorrect and Scoring settings. 
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Save 
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Cluster albums- see post on Manual vs. Autocorrect. Not needed if doing Manual correct but sometimes useful in catching errors/inconsistencies. 
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Review/save 
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Update tags from existing Discogs IDs- depends on having Discogs IDs in MB database. Most tracks don?t have this, but no harm in running this. I only use it to update empty cells from MB so that tag data stays consistent with MB style guidelines. Most useful for art. 
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Correct Lyrics- slow and incomplete but automatic. 
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Save 
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Check compilations/various artists- iTunes uses ?compilation? to refer to a release with more than one artist. iTunes saves compilations to a separate folder from the artist folders it uses for single-artist releases. MB uses ?compilation? in the more traditional sense of a greatest hits release. Since I let iTunes organize & name my files, I conform to the iTunes usage. 
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Fill in disk number- I fill in 1/1 unless otherwise indicated 
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Clear BPM- I don?t use this and delete data found here. 
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Clear comment- I delete extraneous comments. 
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Save 
Duplicate tracks- I identify dupes (same unique ID & same acoustic ID) in Jaikoz, but delete them via iTunes. If I have a whole album that was imported at once, I don?t want to delete one track because there?s a dupe with higher bit rate. Bit rate isn?t conveniently accessible in Jaikoz.
Album Art- the art Jaikoz adds is small (160 x 160 pixels) and pretty low quality. I prefer to add via Discogs or iTunes and embed via a script. Surprisingly (?), iTunes makes a lot of mistakes, particularly with compilations. Much of this is still done manually. I would love it if Jaikoz could find a source of higher quality art so this could be automated. I realize there are licensing issues.
Genre- the classification schemes used in MB and Discogs are so arbitrary as to be useless. I follow the general classification at allmusic.com and try to add in their Style groupings for further precision. Sadly, this is a manual process.