expand ms_meta assayapp functionality

[sellth]

Add Inline linking:

• [x] PROCESS: Protocol file > MiscFiles
• [x] PROCESS: * method file > MiscFiles
• [x] PROCESS: Log file > ResultsReports
• [x] MATERIAL: Derived data file > ResultsReports
• [x] Use SIMPLE_LINK_TEMPLATE for existing raw data file linking

[mikkonie]

Just a note, remember to add related issues when creating a pull request and refer to those issues in the PR.