Updates and refreshes to GIS documentation and landing page

[jshoughtaling]

This PR updates the OHDSI/GIS repository to serve as a central hub for the GIS Working Group, with up-to-date architecture documentation, some project management info, and site build tooling.

Tip

The easiest way to review this PR is to:

1. clone the source repository
   git clone https://github.com/TuftsCTSI/GIS.git
2. load the file - docs/index.html in your local web browser

Major Changes:

1. Architecture Corrections

• Clarified gaiaCore as multi-language connector framework (not R package)
• Documented gaiaDb as the central backend service with all SQL/PostGIS processing logic
• Added gaiaDocker as official deployment orchestration tool
• Updated data flow diagrams and package relationships

2. Developer Documentation (following Hades/chorus-developer patterns)

• Complete developer hub with ecosystem overview
• Package status table with shields.io badges
• Contributing guidelines and code review process
• Technical architecture diagrams and data flows
• Deployment strategies - @jaygee-on-github (Docker, Podman, Ansible, Kubernetes, manual)

3. Component Documentation

• Updated gaiaDb.Rmd and gaiaCore.Rmd with current architecture
• Created gaiaCatalog.Rmd and gaiaDocker.Rmd
• Removed obsolete gaiaOHDSI.Rmd

4. Vocabulary Documentation

• Added comprehensive CVB (Custom Vocabulary Builder) section
• Documented Google Sheets → GitHub → Azure → Delta Tables pipeline
• Integrated SSSOM framework and automated build process

5. Project Management

• Created project-management.Rmd
• Created some GitHub issue automation (.github/action-items/) with a bash script + JSON structure for converting meeting action items to issues

6. Site Build Tooling

• build-site.R script for automated documentation builds
• BUILD.md with comprehensive build instructions
• Updated README with other build info

@TheCedarPrince - note that some of the contribution docs you've talked about are represented here, but there's definitely room for more onboarding info. Would be good to sync on what you're putting together and perhaps we can include in this PR?

Key next steps

• Split gaiaCore PR into a connector-based PR for gaiaCore, and merge the DB routines into a gaiaDB PR (@tibbben - as discussed)
• Cross reference all related issues to this PR

[jaygee-on-github]

You might want to consider additional sections for OMOP CDM changes and an inventory of our use cases.

In a way all the components and their relationships depend on the definition of the external_exposure table and any auxiliary table we might construct on top of it that place these exposures in a time series.

There is a definition "out there" that Polina developed. It doesn't include any auxiliary tables. It could be our first OMOP CDM MVP. Future OMOP CDM MVPs could be driven by use cases.

This is why we might want another section that inventories the use cases and the contribution(s) each might make in the future vis a vis the toolchain. Some of these use cases could be initiatives we are looking to for future MVPs specific to the CDM and additional vocabulary needed to support it.

Beyond the CDM changes there are the analyses that uses cases want to support in new domains the GIS extension places before us -- environmental epidemiology and sociodemographic epidemiology alone or in combination with spatial epidemiology.

Currently we can't depend on ATLAS for analyses. Instead we are depending on the underlying OHDSI Methods Library (HADES). Use cases may want us to grow HADES. Use cases may be developing analyses that they propose OHDSI integrates with HADES in support of one or more of the new research domains that the GIS extension places before us.

Finally, both current and future analyses may require additional transparency across the toolchain beyond what they currently provide in support of ethical analysis. Maybe LLMs with additional prompting or by other means can facilitate here.