Fix hardcoded pantools target dir

Since the distribution of a single jar file for PanTools is hindered by the dependency of the jar file to be located in a specific directory, this is fixed in this merge request.

Still to do:

• Update documentation
• A wild bug appeared: 'alt_id' is overwritten when buidling the GO hierarchy, even though a GO identifier can have multiple 'alt_id's (edit: part of !118 (merged))
• Another wild bug appeared: pantools msa --method functions with a GO term only searches for a match with the 'id' of a GO term, not its 'alt_id'. (edit: part of !118 (merged))
• Update CHANGELOG.md

Closes #32 (closed) when merged.

assigned to @worku005

added 1 commit

• a1c7f716 - found bug with alt_id for GO nodes

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added 3 commits

• a1c7f716...d88e829f - 2 commits from branch develop
• bc3d1a55 - merge develop into fix_hardcoded_pantools_target_dir

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changed the description

changed the description

added 1 commit

• 878270b3 - fixed some ugly lines of code

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added 2 commits

• 0776d21e - update CHANGELOG
• 9cfee7d2 - updating documentation for add_functions -D

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marked the checklist item Update documentation as completed

marked the checklist item Update CHANGELOG.md as completed

requested review from @jonkh004

mentioned in merge request !118 (merged)

added 3 commits

• 1c40dc74 - making functional annotations databases directory optional with default location
• 04b665d5 - update example commands for add_functions
• 08bb0f81 - update documentation with change of making functional databases directory optional

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changed the description

resolved all threads

marked this merge request as ready

added 3 commits

• 08bb0f81...c7a337fb - 2 commits from branch develop
• 71b35110 - merge develop into fix_hardcoded_pantools_target_dir

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marked the checklist item A wild bug appeared: 'alt_id' is overwritten when buidling the GO hierarchy, even though a GO identifier can have multiple 'alt_id's (edit: part of !118 (merged)) as completed