Git source files and No such file or directory

This seems to be your problem:

(flatpak-builder:1135937): flatpak-builder-WARNING **: 14:56:24.915: Invalid source: No slashes allowed in dest-filename

Modules Script Failing on Flathub, worked fine 3 months ago
flatpak-builder 1.0.14 breaks build of org.libreoffice.LibreOffice, empty /run/build/libreoffice

You have to remove the relative path from dest-filename:

{
  "type": "file",
  "path": "sources/pjproject-2.10.tar.gz",
  "dest-filename": "deps/2.10.tar.gz"
},

becomes

{
  "type": "file",
  "path": "sources/pjproject-2.10.tar.gz",
  "dest": "deps"
  "dest-filename": "2.10.tar.gz"
},