docs: audit-driven URL fixes (Jammy2211 → PyAutoLabs, /release/ → /main/, etc.) (#413)

Apply scripted URL rewrites surfaced by the new
admin_jammy/software/url_check/ audit tool. All changes are doc-only
(README, *.md, *.rst, plus docstring URLs in source files). No
behaviour changes. Line endings preserved.

Patterns applied:
- hhttps:// → https:// (user-reported typo in overview_2_new_user_guide.md)
- Jammy2211/<workspace> → PyAutoLabs/<workspace> (workspaces migrated orgs)
- Jammy2211|rhayes777/<library> → PyAutoLabs/<library>
- /blob/release/ and /tree/release/ → /main/ (release branch removed)
- joshspeagle/nautilus → johannesulf/nautilus (sampler moved orgs)
- rhayes777/PyAutoBuild → PyAutoLabs/PyAutoBuild
- bokeh CoC moved to /docs/CODE_OF_CONDUCT.md
- numfocus CoC moved to numfocus.org/code-of-conduct
- www.sphinx-doc.org /en/main → /en/master
- pyautofit.readthedocs.io renames (cookbook_1_basics → cookbooks/model,
  overview/model_fit → overview/the_basics, etc.)
- autofit_workspace overview/{simple,complex}/{fit,result}.ipynb → new flat structure
- workspaces modeling/imaging/features/<x>.ipynb → imaging/features/<x>/modeling.ipynb
- workspaces multi/modeling/features/<x>.ipynb → multi/features/<x>/modeling.ipynb
- workspaces multi/modeling/start_here.ipynb → multi/start_here.ipynb
- workspaces tree/main/notebooks/plot → notebooks/guides/plot
- Colab badge URL: workspace-root start_here.ipynb → notebooks/<type>/start_here.ipynb

Tool + report: PyAutoLabs/admin_jammy#21
Issue: PyAutoLabs/PyAutoLens#508

Co-authored-by: Jammy2211 <JNightingale2211@gmail.com>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: 3 people

CITATIONS.md

@@ -1,9 +1,9 @@
 # Citations & References
 
 The bibtex entries for **PyAutoGalaxy** and its affiliated software packages can be found
-[here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.bib), with example text for citing **PyAutoGalaxy**
-in [.tex format here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.tex) format here and
-[.md format here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.md).
+[here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.bib), with example text for citing **PyAutoGalaxy**
+in [.tex format here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.tex) format here and
+[.md format here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.md).
 
 As shown in the examples, we would greatly appreciate it if you mention **PyAutoGalaxy** by name and include a link to
 our GitHub page!

CODE_OF_CONDUCT.md

@@ -301,7 +301,7 @@ the situation is not yet resolved.
 
 ## License
 
-This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://github.com/numfocus/numfocus/blob/main/manual/numfocus-coc.md#the-short-version),
-which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/main/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/main/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct).
+This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://numfocus.org/code-of-conduct),
+which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/main/docs/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/main/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct).
 
 **PyAutoGalaxy Code of Conduct is licensed under the [Creative Commons Attribution 3.0 Unported License](https://creativecommons.org/licenses/by/3.0/).**

CONTRIBUTING.md

@@ -74,7 +74,7 @@ Contributions are welcome and greatly appreciated!
 
 ### Report Bugs
 
-Report bugs at https://github.com/Jammy2211/PyAutoGalaxy/issues
+Report bugs at https://github.com/PyAutoLabs/PyAutoGalaxy/issues
 
 If you are playing with the PyAutoGalaxy library and find a bug, please
 reporting it including:
@@ -86,7 +86,7 @@ reporting it including:
 ### Propose New Features
 
 The best way to send feedback is to open an issue at
-https://github.com/Jammy2211/PyAutoGalaxy
+https://github.com/PyAutoLabs/PyAutoGalaxy
 with tag *enhancement*.
 
 If you are proposing a nnew feature:

README.md

@@ -1,8 +1,8 @@
 # PyAutoGalaxy: Open-Source Multi Wavelength Galaxy Structure & Morphology
 
-[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/start_here.ipynb)
+[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/notebooks/imaging/start_here.ipynb)
 [![Documentation Status](https://readthedocs.org/projects/pyautogalaxy/badge/?version=latest)](https://pyautogalaxy.readthedocs.io/en/latest/?badge=latest)
-[![Tests](https://github.com/Jammy2211/PyAutoGalaxy/actions/workflows/main.yml/badge.svg)](https://github.com/Jammy2211/PyAutoGalaxy/actions)
+[![Tests](https://github.com/PyAutoLabs/PyAutoGalaxy/actions/workflows/main.yml/badge.svg)](https://github.com/PyAutoLabs/PyAutoGalaxy/actions)
 [![Build](https://github.com/Jammy2211/PyAutoBuild/actions/workflows/release.yml/badge.svg)](https://github.com/Jammy2211/PyAutoBuild/actions)
 [![Code Style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![JOSS](https://joss.theoj.org/papers/10.21105/joss.04475/status.svg)](https://doi.org/10.21105/joss.04475)
@@ -14,23 +14,23 @@
 
 [Installation Guide](https://pyautogalaxy.readthedocs.io/en/latest/installation/overview.html) |
 [readthedocs](https://pyautogalaxy.readthedocs.io/en/latest/index.html) |
-[Introduction on Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/start_here.ipynb) |
+[Introduction on Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/notebooks/imaging/start_here.ipynb) |
 [HowToGalaxy](https://pyautogalaxy.readthedocs.io/en/latest/howtogalaxy/howtogalaxy.html)
 
 **PyAutoGalaxy** is software for analysing the morphologies and structures of galaxies:
 
-[![HST Combined](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/hstcombined.png?raw=true)](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/hstcombined.png)
+[![HST Combined](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/paper/hstcombined.png?raw=true)](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/paper/hstcombined.png)
 
 **PyAutoGalaxy** also fits interferometer data from observatories such as ALMA:
 
-[![ALMA Combined](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/almacombined.png?raw=true)](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/almacombined.png)
+[![ALMA Combined](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/paper/almacombined.png?raw=true)](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/paper/almacombined.png)
 
 ## Getting Started
 
 The following links are useful for new starters:
 
 - [The PyAutoGalaxy readthedocs](https://pyautogalaxy.readthedocs.io/en/latest), which includes [an overview of PyAutoGalaxy's core features](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_start_here.html), [a new user starting guide](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_2_new_user_guide.html) and [an installation guide](https://pyautogalaxy.readthedocs.io/en/latest/installation/overview.html).
-- [The introduction Jupyter Notebook on Google Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/start_here.ipynb), where you can try **PyAutoGalaxy** in a web browser (without installation).
+- [The introduction Jupyter Notebook on Google Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/notebooks/imaging/start_here.ipynb), where you can try **PyAutoGalaxy** in a web browser (without installation).
 - [The autogalaxy_workspace GitHub repository](https://github.com/PyAutoLabs/autogalaxy_workspace): example scripts covering every **PyAutoGalaxy** use case.
 - [The HowToGalaxy GitHub repository](https://github.com/PyAutoLabs/HowToGalaxy): a Jupyter notebook lecture series teaching galaxy modeling from the ground up.
 
@@ -51,7 +51,7 @@ galaxy modeling and analysis, and helps troubleshoot problems.
 
 Slack is invitation-only. If you'd like to join, please send an email requesting an invite.
 
-For installation issues, bug reports, or feature requests, please raise an issue on the [GitHub issues page](https://github.com/Jammy2211/PyAutoGalaxy/issues).
+For installation issues, bug reports, or feature requests, please raise an issue on the [GitHub issues page](https://github.com/PyAutoLabs/PyAutoGalaxy/issues).
 
 ## HowToGalaxy
 
@@ -63,10 +63,10 @@ A complete overview of the lectures [is provided on the HowToGalaxy readthedocs
 
 ## Citations
 
-Information on how to cite **PyAutoGalaxy** in publications can be found [on the citations page](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/CITATIONS.md).
+Information on how to cite **PyAutoGalaxy** in publications can be found [on the citations page](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/CITATIONS.md).
 
 ## Contributing
 
-Information on how to contribute to **PyAutoGalaxy** can be found [on the contributing page](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/CONTRIBUTING.md).
+Information on how to contribute to **PyAutoGalaxy** can be found [on the contributing page](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/CONTRIBUTING.md).
 
 Hands on support for contributions is available via our Slack workspace, again please email to request an invite.

docs/api/plot.rst

@@ -5,12 +5,12 @@ Plotting
 **PyAutoGalaxy** custom visualization library.
 
 Step-by-step Juypter notebook guides illustrating all objects listed on this page are
-provided on the `autogalaxy_workspace: plot tutorials <https://github.com/Jammy2211/autogalaxy_workspace/tree/release/notebooks/plot>`_ and
+provided on the `autogalaxy_workspace: plot tutorials <https://github.com/PyAutoLabs/autogalaxy_workspace/tree/main/notebooks/guides/plot>`_ and
 it is strongly recommended you use those to learn plot customization.
 
 **Examples / Tutorials:**
 
-- `autogalaxy_workspace: plot tutorials <https://github.com/Jammy2211/autogalaxy_workspace/tree/release/notebooks/plot>`_
+- `autogalaxy_workspace: plot tutorials <https://github.com/PyAutoLabs/autogalaxy_workspace/tree/main/notebooks/guides/plot>`_
 
 Plotters [aplt]
 ---------------

docs/conf.py

@@ -4,7 +4,7 @@
 #
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
-# https://www.sphinx-doc.org/en/main/usage/configuration.html
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
 
@@ -65,7 +65,7 @@
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
-    "sphinx": ("https://www.sphinx-doc.org/en/main", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master", None),
 }
 
 # -- Options for TODOs -------------------------------------------------------

docs/general/citations.md

@@ -3,9 +3,9 @@
 # Citations & References
 
 The bibtex entries for **PyAutoGalaxy** and its affiliated software packages can be found
-[here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.bib), with example text for citing **PyAutoGalaxy**
-in [.tex format here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.tex) format here and
-[.md format here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.md).
+[here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.bib), with example text for citing **PyAutoGalaxy**
+in [.tex format here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.tex) format here and
+[.md format here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.md).
 
 **PyAutoGalaxy** is published in the [Journal of Open Source Software](https://joss.theoj.org/papers/10.21105/joss.04475#) and its
 entry in the above .bib file is under the citation key `pyautogalaxy`.

docs/general/configs.md

@@ -4,7 +4,7 @@
 visualization and other aspects of **PyAutoGalaxy**.
 
 Descriptions of every configuration file and their input parameters are provided in the `README.md` in
-the [config directory of the workspace](https://github.com/Jammy2211/autogalaxy_workspace/tree/release/config)
+the [config directory of the workspace](https://github.com/PyAutoLabs/autogalaxy_workspace/tree/main/config)
 
 ## Setup
 

docs/general/credits.md

@@ -6,7 +6,7 @@
 
 [James Nightingale](https://github.com/Jammy2211): Lead developer & PyAutoGalaxy guru.
 
-[Richard Hayes](https://github.com/rhayes777): Lead developer & [PyAutoFit](https://github.com/rhayes777/PyAutoFit) guru.
+[Richard Hayes](https://github.com/rhayes777): Lead developer & [PyAutoFit](https://github.com/PyAutoLabs/PyAutoFit) guru.
 
 [Aristeidis Amvrosiadis](https://github.com/Sketos): Interferometer Analysis.
 

docs/general/model_cookbook.md

@@ -224,16 +224,16 @@ profiles.
 
 The following example notebooks show how to compose and fit these models:
 
-<https://github.com/Jammy2211/autogalaxy_workspace/blob/release/notebooks/modeling/imaging/features/multi_gaussian_expansion.ipynb>
-<https://github.com/Jammy2211/autogalaxy_workspace/blob/release/notebooks/modeling/imaging/features/shapelets.ipynb>
+<https://github.com/PyAutoLabs/autogalaxy_workspace/blob/main/notebooks/imaging/features/multi_gaussian_expansion/modeling.ipynb>
+<https://github.com/PyAutoLabs/autogalaxy_workspace/blob/main/notebooks/imaging/features/shapelets/modeling.ipynb>
 
 ## Model Linking (Advanced)
 
 When performing non-linear search chaining, the inferred model of one phase can be linked to the model.
 
 The following example notebooks show how to compose and fit these models:
 
-<https://github.com/Jammy2211/autogalaxy_workspace/blob/release/notebooks/imaging/advanced/chaining/start_here.ipynb>
+<https://github.com/PyAutoLabs/autogalaxy_workspace/blob/main/notebooks/imaging/advanced/chaining/start_here.ipynb>
 
 ## Across Datasets (Advanced)
 
@@ -242,7 +242,7 @@ but certain parameters are free to vary across the datasets.
 
 The following example notebooks show how to compose and fit these models:
 
-<https://github.com/Jammy2211/autogalaxy_workspace/blob/release/notebooks/multi/modeling/start_here.ipynb>
+<https://github.com/PyAutoLabs/autogalaxy_workspace/blob/main/notebooks/multi/start_here.ipynb>
 
 ## Relations (Advanced)
 
@@ -251,7 +251,7 @@ We can compose models where the free parameter(s) vary according to a user-speci
 
 The following example notebooks show how to compose and fit these models:
 
-<https://github.com/Jammy2211/autogalaxy_workspace/blob/release/notebooks/multi/modeling/features/wavelength_dependence.ipynb>
+<https://github.com/PyAutoLabs/autogalaxy_workspace/blob/main/notebooks/multi/features/wavelength_dependence/modeling.ipynb>
 
 ## PyAutoFit API