Design works in 2.4.2 fails with 3.0.0.dev39 ( Overlap errors )

Description

The design is here : https://github.com/MichaelBell/ttsky25b-femtorv-soc.git
It includes some hard-marcro ( not sure if the problem is related to those ).

It works fine with 2.4.2 which is the default for tinytapeout, but when I tried building with 3.0.0.dev39, it fails LVS and reports illegal overlaps.

Switching to extraction from GDS ( MAGIC_EXT_GDS ) fixes the issue.

I didn't investigate the problem further at this time.

The design is a TT design so the config.json is usually generated from the TT tools, I've included what gets generated below :
config_merged.json.txt

Expected Behavior

That it works on 3.0.0dev39 as it does in 2.4.2 :)

Environment report

kernel: Linux
kernel_version: 5.10.0-19-cloud-amd64
supported: True
distro: debian
distro_version: 11
python_version: 3.12.10
python_path:
  - /nix/store/52gxiqi85kkrwiahb85rvq1hx33ckymg-python3.12-librelane-3.0.0.dev39/bin
  - /nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python312.zip
  - /nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12
  - /nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/lib-dynload
  - /nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/site-packages
  - /nix/store/p1iwjlvmsjzi9j2m3jsvxcp3v4ni19ds-python3-3.12.10-env/lib/python3.12/site-packages
  - /nix/store/52gxiqi85kkrwiahb85rvq1hx33ckymg-python3.12-librelane-3.0.0.dev39/lib/python3.12/site-packages
  - /nix/store/k6xkvkwfw2yfnannsqh5ynpsfc4cs8fh-python3.12-click-8.1.8/lib/python3.12/site-packages
  - /nix/store/jb76fp77iljrwnvfkv59rz24xrdjsljf-python3.12-cloup-3.0.7/lib/python3.12/site-packages
  - /nix/store/31639aa7g91847pds9bs1mb3gadw8wgy-python3.12-pyyaml-6.0.2/lib/python3.12/site-packages
  - /nix/store/ca3z4y19sh92xknw9hr4fpcjkmmnawk9-python3.12-yamlcore-0.0.2/lib/python3.12/site-packages
  - /nix/store/hrr207zghhvwy1z20ppk1k9lmif7v2fg-python3.12-rich-14.0.0/lib/python3.12/site-packages
  - /nix/store/aykajibj4whywjjkkiqawck84cnp5byb-python3.12-markdown-it-py-3.0.0/lib/python3.12/site-packages
  - /nix/store/97qkar1kz5rkvrmf4im9xacvkd16q31w-python3.12-mdurl-0.1.2/lib/python3.12/site-packages
  - /nix/store/163nw6jgnnnfhpy2f2qjnwc6lm26ny76-python3.12-pygments-2.19.1/lib/python3.12/site-packages
  - /nix/store/0lln9m37mw7cjdf02krfpiwd4clwdlwl-python3.12-requests-2.32.3/lib/python3.12/site-packages
  - /nix/store/y85rrr4sx62x27fka04sncbbd7g8g59j-python3.12-certifi-2025.01.31/lib/python3.12/site-packages
  - /nix/store/azbbrwb8glahagaqqsaa4akv20903lm3-python3.12-charset-normalizer-3.4.1/lib/python3.12/site-packages
  - /nix/store/n0v27hx3n5sc51z833jbmkgi4sm086qg-python3.12-idna-3.10/lib/python3.12/site-packages
  - /nix/store/lf8ilk72n59c1yg7zbwvqd5mimlqzpqk-python3.12-urllib3-2.3.0/lib/python3.12/site-packages
  - /nix/store/jbrc285igc9lyzbxaykqq668vvdcdsh0-python3.12-pcpp-1.30/lib/python3.12/site-packages
  - /nix/store/09fnsvr92v4qckqfp91fg4hrql4cmz0c-python3.12-ciel-2.2.0/lib/python3.12/site-packages
  - /nix/store/fh5pvazqpn19q9vi46aiwv1c8lvj7i15-python3.12-httpx-0.28.1/lib/python3.12/site-packages
  - /nix/store/6bgklsghip01ajabmn05jg9j5n059552-python3.12-anyio-4.9.0/lib/python3.12/site-packages
  - /nix/store/jbzhj74lhh2v3cjk1r1f8icpk9d20g6r-python3.12-sniffio-1.3.1/lib/python3.12/site-packages
  - /nix/store/d52qvak789g813n4nb8ghlsvi2r2yifh-python3.12-typing-extensions-4.13.2/lib/python3.12/site-packages
  - /nix/store/gmwf71m0vhbcsmpdgljhqd4x8ljixld1-python3.12-httpcore-1.0.9/lib/python3.12/site-packages
  - /nix/store/ib7958qxra4bw6jm9aj8hzsri8cpwp56-python3.12-h11-0.16.0/lib/python3.12/site-packages
  - /nix/store/js77mbaifiifrdpfbq2jwvrj58j6skfb-python3.12-zstandard-0.23.0/lib/python3.12/site-packages
  - /nix/store/w56z2iwqp4c3k0bx1rnh2kkmh8jysk48-python3.12-cffi-1.17.1/lib/python3.12/site-packages
  - /nix/store/mhscxvpf98amzkih54jyhqpw7xx6i5lc-python3.12-pycparser-2.22/lib/python3.12/site-packages
  - /nix/store/avvw0a5j8lykr1079c90k563bpsq7zqw-python3.12-truststore-0.10.1/lib/python3.12/site-packages
  - /nix/store/v48ygs786b4kb4vdiin2p44n2zlv9npj-python3.12-aiohttp-3.11.15/lib/python3.12/site-packages
  - /nix/store/c5icf92skq3nwc32mn4gm6dfjhyh69dn-python3.12-aiohappyeyeballs-2.6.1/lib/python3.12/site-packages
  - /nix/store/8nkvrfkhwyz1p9dndpihbwjimr2h7r9b-python3.12-aiosignal-1.3.2/lib/python3.12/site-packages
  - /nix/store/lc7sz0nqh85l9hf2a6rhg1g75bv94m1p-python3.12-frozenlist-1.5.0/lib/python3.12/site-packages
  - /nix/store/bmmj3s98iwxv78dp8qmdg4s2h8wy84ln-python3.12-async-timeout-5.0.1/lib/python3.12/site-packages
  - /nix/store/blsxhz45in0asxiq6frv665aq8vzvnx7-python3.12-attrs-25.3.0/lib/python3.12/site-packages
  - /nix/store/anfi764nrpzcsjildr7hwzx0d964xq78-python3.12-multidict-6.2.0/lib/python3.12/site-packages
  - /nix/store/pa28335hmjralxb0vhpqz83k2xz9sp3y-python3.12-propcache-0.3.1/lib/python3.12/site-packages
  - /nix/store/h0lzas15y5mxk9r72n7sc18dg801nvi8-python3.12-yarl-1.18.3/lib/python3.12/site-packages
  - /nix/store/m5rmrc3imjqxgs5400g10h26yawfl5w5-python3.12-aiodns-3.2.0/lib/python3.12/site-packages
  - /nix/store/s5bqhp041321b0iqwbaysaaiirr97m09-python3.12-pycares-4.5.0/lib/python3.12/site-packages
  - /nix/store/xig5nxjhxf419kwbsay8fdbzkhnnqics-python3.12-brotli-1.1.0/lib/python3.12/site-packages
  - /nix/store/vg7494b4p4if8a126w3ickkphc559idb-python3.12-cryptography-44.0.2/lib/python3.12/site-packages
  - /nix/store/mkp46h7s9s67c3h821l8i78f9qh7b6y1-python3.12-pyopenssl-25.0.0/lib/python3.12/site-packages
  - /nix/store/h4ql4f7cbg29v8dxyjfv5aaawqva0ckn-python3.12-trustme-1.2.1/lib/python3.12/site-packages
  - /nix/store/4y1dsgr9q2ng9y3s1d5jwarc7afj313w-python3.12-socksio-1.0.0/lib/python3.12/site-packages
  - /nix/store/098rbi42h9b0bb7iyzc2vi87vcfi6k0g-python3.12-tkinter-3.12.10/lib/python3.12/site-packages
  - /nix/store/g41zzs5fh97rw2qn6ixbz314b23h902j-python3.12-lxml-5.3.1/lib/python3.12/site-packages
  - /nix/store/15nabrbrj0wl071jjbvzmpb1l9fw2dpb-python3.12-deprecated-1.2.18/lib/python3.12/site-packages
  - /nix/store/nby49z3h8g7b7kl8c75h2cdiwy5q2n13-python3.12-wrapt-1.17.2/lib/python3.12/site-packages
  - /nix/store/11j40pn2wv6vwh7q3rfl0ardnrxa1ady-python3.12-libparse-0.56.0/lib/python3.12/site-packages
  - /nix/store/ny3v2j2cxx3flyd2gfbvgkcb0v84wf67-python3.12-psutil-7.0.0/lib/python3.12/site-packages
  - /nix/store/qz6hrqnmpsvvz6lvqw73a1wbx6ac42k1-klayout-0.30.2-python/lib/python3.12/site-packages
  - /nix/store/gj0bwzpq6ck90r7kjjgmcr9qqx7fbi5w-python3.12-rapidfuzz-3.13.0/lib/python3.12/site-packages
  - /nix/store/4l4d52ad631s7ap3wqcj4war1cy4zyd5-python3.12-semver-3.0.4/lib/python3.12/site-packages
tkinter: True
container_info:
  engine: docker
  version: 27.3.1
  conmon: False
  rootless: False
  seccomp: False
  selinux: False
  apparmor: False
  path: /usr/bin/docker
nix_info:
  version_string: nix (Nix) 2.24.5
  channels:
  nix_command: True
  flakes: True

Reproduction material

reproducible.tar.gz

Relevant log output

N/A

Start with reproducible.tar.gz and config_merged.json.txt, then compare the LVS and extraction behavior between 2.4.2 and 3.0.0.dev39, focusing on the MAGIC_EXT_GDS setting and the reported overlap errors. Done means the supplied design completes LVS on 3.0.0.dev39 without requiring GDS extraction as a workaround.