Resolve "Replace deprecated APIs"

Closes #688 (closed)

changed milestone to %v14.0.0~alpha.0

added dev-todo refactor labels

added 53 commits

• 27741bf3...63d7d1c1 - 4 commits from branch master
• c2eae2de - class types are better resolved where doable
• 3a8177b0 - EnumComparator uses proper generic parameters
• 902260fa - unused code removed
• 211fd49f - create user doesn't use global variable
• cd0e66bd - comments unit tests merged into one file
• 9a91f723 - ElementDao tests merged
• 09dcd5b1 - unused test function removed
• ad2d04b5 - daos moved to proper test files
• 14526055 - deprecated Query inerface replaced
• 23b5e200 - imports organized
• 150b445c - Flyway deprecated api removed
• c1a3aa50 - old unused code removed
• 1feef777 - old unused method removed
• 0838c67f - deprecatedmethodremoved
• 2191b079 - deprecated method removed
• 6718734a - weirdjava construct removed
• ed72d739 - deprecated APIcallsremoved
• d16dab7b - deprecatedmethodcallremoved
• 198ce019 - default version UIDadded
• bc3111df - spring password encoders are used
• 1146be0c - unused fields removed
• 7eb625a0 - toString function takes default charset as second argument
• dc72db58 - old api call removed
• 63e6b8e2 - missing parameter added
• 69b59f09 - SQLQuery replaced with NativeQuery
• 320fc51c - NoOpPasswordEncoder removed
• caf12fff - remove of old sbgnml command line util - the functionality is available via API
• 8b3f37c8 - build of sbgnml module fixed
• 4bfbde43 - unused code removed
• a987cda7 - deprecated api replaced with new calls
• cd3a7f25 - obsolete spring security constrocutor replaced
• 71b309f1 - obsolete criteria replaced
• 1c45fb44 - deprecated criteria api replaced
• 88f2896a - mvn creates ar with *.js, *.css, *.map files build by npm
• 01784225 - instead of copying from outside of maven module we are exploding jar file with...
• 12c56c86 - Merge branch 'master' into 469-debian-package-use-dbconfig-common
• 5675ccfa - surefire plugin requires additional options to work on jdk 11
• b5de2ac6 - minor/patch dependencies updates
• ed4973ba - dependency conflicts resolved
• f6ed0faf - ssl turned of on miriam connector due to problem with server certificate
• f394acab - unused test files from annotation module removed
• c84c9c1a - unused test files in CD converter removed
• 4162173b - removed unused sbml test file
• 06792baf - unused converter testfile removed
• 7ef5058c - removed unused test file for wikipathways
• 4f99fe6a - unused reactome test files removed
• 60ccd7fc - unused rest test files
• 32127773 - unused web tet files removed
• 757efa25 - unused service test files removed

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added 1 commit

• 844f4477 - surefire argument removed

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added 1 commit

• b7503cba - dependency conflicts resolved

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added 2 commits

• 7362d66f - java 11 is not supported yet
• 6538c9a3 - spring upgraded

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added 4 commits

• 8456ccc0 - old editor module removed
• cb23e257 - old unused reactome code removed - if needed it should be transformed into a plugin
• a3b8a80c - old unused quadtrees implementation removed
• 72778f58 - gitlab ci upgraded after modules removal

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added 3 commits

• 3e308282 - for some reason logger started behaving weirdly
• eb499b5e - missing promise is now awaited for
• a49f8f70 - unused code in commons removed

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added 3 commits

• 48d835d4 - unused fields removed
• 3b6fc51a - deprecated abstract class removed
• 6d197eb4 - loggers should be private

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unmarked as a Work In Progress

enabled an automatic merge when the pipeline for 6d197eb4 succeeds

mentioned in commit 4fbe6ba9

merged