You can delete the old memory layouts they won't work with the current DT anyway. But I don't see why it would stop reading the directory after the old ones. You should check the other paths in the list: the <appdir>/<workdir> ones may not be in locate search paths.
so I fiddled around with it a bit, deleting the entire folder in /usr/local/share certainly got noticed and DT wouldn't start anymore. I put it back in with only the new files (0.44.02 to .05) and, well, this happened:
2018-Jan.-17 12:17:00.275 INFO core Dwarf Therapist "39.1.2" starting normally. [/DF/Dwarf-Therapist-master/src/dwarftherapist.cpp:186] (setup_logging)
2018-Jan.-17 12:17:00.276 INFO core Runtime QT Version 5.5.1 [/DF/Dwarf-Therapist-master/src/dwarftherapist.cpp:187] (setup_logging)
2018-Jan.-17 12:17:02.359 INFO core beginning to read settings [/DF/Dwarf-Therapist-master/src/dwarftherapist.cpp:213] (read_settings)
2018-Jan.-17 12:17:02.396 INFO core finished reading settings [/DF/Dwarf-Therapist-master/src/dwarftherapist.cpp:264] (read_settings)
2018-Jan.-17 12:17:02.489 INFO core attempting connection to running DF game [/DF/Dwarf-Therapist-master/src/mainwindow.cpp:405] (connect_to_df)
2018-Jan.-17 12:17:02.492 INFO core adding valid layout "v0.40.24" checksum: "0xc42f5594" SHA: "643ab3ad090fc9c43093ce44710f2869ece8f279" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.494 INFO core adding valid layout "v0.40.23" checksum: "0x02ae0bd7" SHA: "17cda707d15ade3160f2a900078222303fcdbd05" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.497 INFO core adding valid layout "v0.40.22" checksum: "0xec989a28" SHA: "1b5e3172e086f0557bc7428eab86fae766058a13" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.499 INFO core adding valid layout "v0.40.21" checksum: "0x0c517807" SHA: "81b8b25690d82e400b25956699debb852182d8b7" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.501 INFO core adding valid layout "v0.40.20" checksum: "0xc281d937" SHA: "552415150aa4d315d8eee188b76e436b6a6cd167" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.504 INFO core adding valid layout "v0.40.19" checksum: "0xb7bbe8a5" SHA: "3b31e792240e01eba2a621273e8b582a93ecfa60" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.506 INFO core adding valid layout "v0.40.18" checksum: "0x25b761ee" SHA: "a9f2cbb0c83a507e475c9f02230bdb97b5f4c6af" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.509 INFO core adding valid layout "v0.40.16" checksum: "0x13cc404f" SHA: "0afc4fbbded75ee17db72482d64985815cf5cd19" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.511 INFO core adding valid layout "v0.40.15" checksum: "0xf1049a2b" SHA: "693e0ad029fd94ebd2cee92e57bc2c0d7ae83298" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.513 INFO core adding valid layout "v0.40.14" checksum: "0x8ab84807" SHA: "df02ce403eddd80c95dccbab7c14019fd2289aaa" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.516 INFO core adding valid layout "v0.40.13" checksum: "0xdb688bd7" SHA: "66e5b841f7a77a9acb0271d26bbb428bd2a8bc77" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.518 INFO core adding valid layout "v0.40.12" checksum: "0x5ad26cb2" SHA: "440e254cb16e74053a45adf7b4459be77fd3b470" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.520 INFO core adding valid layout "v0.40.11" checksum: "0xffde0733" SHA: "717ce58409dfaa496e64f3a13ec247a42e1d5f15" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.523 INFO core adding valid layout "v0.40.10" checksum: "0x0b7185da" SHA: "229ad028ead95871d5f346893e3b9616d9e81c04" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.525 INFO core adding valid layout "v0.40.09" checksum: "0x9e592efe" SHA: "c3e49e0a755f24d3128d5363e3c37468407d756c" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.528 INFO core adding valid layout "v0.40.08" checksum: "0xa2f83bf8" SHA: "90782ee72b411e9da8f689612629421ecb7c4b16" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.530 INFO core adding valid layout "v0.40.07" checksum: "0x4d274c4d" SHA: "1d84ae31a44e3a1547b5dcc46730bea7adb72851" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.532 INFO core adding valid layout "v0.40.06" checksum: "0x569f6c42" SHA: "5dcfba396ec18d2b77065798bc04a06bc609c62b" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.535 INFO core adding valid layout "v0.40.05" checksum: "0x5612460b" SHA: "f1bc5eb8978a946a057e8eb74bef10e73bd9b621" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.537 INFO core adding valid layout "v0.40.04" checksum: "0x9fdc4a78" SHA: "ce88fd2113291077a64e94cd9fa1ac5d1f15d830" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.539 INFO core adding valid layout "v0.40.03" checksum: "0xdd544df6" SHA: "3d3621795b6b01c018eb4a2de6888750ba0050ab" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.541 INFO core adding valid layout "v0.40.01" checksum: "0xd3460da2" SHA: "d4125328b21f5312af9215303df3a0a55033ae87" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:106] (DFInstance)
2018-Jan.-17 12:17:02.553 INFO core Dwarf fortress path: "/DF/df_linux" [/DF/Dwarf-Therapist-master/src/dfinstancelinux.cpp:262] (find_running_copy)
2018-Jan.-17 12:17:02.661 INFO core Setting memory layout for DF checksum "0xcfe90090" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:1081] (set_memory_layout)
2018-Jan.-17 12:17:02.661 INFO core Could not find layout for checksum "0xcfe90090" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:1104] (get_memory_layout)
2018-Jan.-17 12:17:02.661 INFO core Checking for layout for checksum: "0xcfe90090" [/DF/Dwarf-Therapist-master/src/updater.cpp:133] (check_layouts)
2018-Jan.-17 12:17:03.388 INFO core Setting memory layout for DF checksum "0xcfe90090" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:1081] (set_memory_layout)
2018-Jan.-17 12:17:03.388 INFO core Could not find layout for checksum "0xcfe90090" [/DF/Dwarf-Therapist-master/src/dfinstance.cpp:1104] (get_memory_layout)
2018-Jan.-17 12:17:03.388 WARNING core lost connection to DF [/home/achanei/Desktop/DF/Dwarf-Therapist-master/src/mainwindow.cpp:466] (lost_df_connection)
2018-Jan.-17 12:17:03.398 ERROR core ("Unidentified Game Version", "I'm sorry but I don't know how to talk to this version of Dwarf Fortress!", "Checksum: 0xcfe90090", "Supported Versions:\nv0.40.24 (0xc42f5594)\nv0.40.23 (0x02ae0bd7)\nv0.40.22 (0xec989a28)\nv0.40.21 (0x0c517807)\nv0.40.20 (0xc281d937)\nv0.40.19 (0xb7bbe8a5)\nv0.40.18 (0x25b761ee)\nv0.40.16 (0x13cc404f)\nv0.40.15 (0xf1049a2b)\nv0.40.14 (0x8ab84807)\nv0.40.13 (0xdb688bd7)\nv0.40.12 (0x5ad26cb2)\nv0.40.11 (0xffde0733)\nv0.40.10 (0x0b7185da)\nv0.40.09 (0x9e592efe)\nv0.40.08 (0xa2f83bf8)\nv0.40.07 (0x4d274c4d)\nv0.40.06 (0x569f6c42)\nv0.40.05 (0x5612460b)\nv0.40.04 (0x9fdc4a78)\nv0.40.03 (0xdd544df6)\nv0.40.01 (0xd3460da2)") [/DF/Dwarf-Therapist-master/src/mainwindow.cpp:488] (lost_df_connection)
So yeah, you are right, those files are coming from somewhere else, they certainly aren't back in the usr/local/share directory. Guess i'll run find, see what turns up
EDIT:
Got it! home/$user/.local/share was the culprit, find turned up a dwarftherapist memory layouts folder there, and replacing the 0.40.x files there with the current one made it work. Awesome!
Pretty sure the problem was indeed the multiple old versions of DT I had used years ago, combined with the fact that DT stops looking after finding one set of memory layouts. The perils of playing the same game over and over again as new versions come out, I suppose.
Thank you and everyone else for the help, I really appreciate it - fort mode is basically unplayble without DT. Happy to know it is possible to get the game going on a linux machine!