Improve experience of docify scaffold and the eventual static website deployment of multiple scaffolded architectures.

## Background

As discussed on https://github.com/finos/architecture-as-code/issues/2039 as part of the demo of the create website mode [pull/2061](https://github.com/finos/architecture-as-code/pulls/2061), post scaffolding, deployment becomes a bit fiddly for the end user as they still require a reference to the architecture file which can only be found in the front-matter of scaffolded files.

In addition, if multiple architecture files had been scaffolded, one may want to deploy one website from those generated files, rather than deploy distinct websites per architecture.

Per suggestion from @rocketstack-matt, we could look to split the current "Create Website" workflow into two distinct phases:
1. Scaffold phase: Generate content pages and an `index.json` manifest describing the site structure
2. Deploy phase: Generate Docusaurus configuration files (`sidebars.js`, `package.json`, `docusaurus.config.js`) from the manifest leveraging the index.json file (this can be altered by the user

This allows users to customize the site structure before generating the deployment configuration.

## Problem Statement

Currently, `docify --scaffold` generates both:
- Content pages (`docs/nodes/*.md`, `docs/relationships/*.md`)
- Docusaurus configuration (`package.json`, `sidebars.js`, `docusaurus.config.js`)

This creates friction when users want to:
- Customize which pages appear in the sidebar
- Reorder navigation items
- Add custom pages not generated from the architecture
- Review the site structure before committing to a deployment configuration

## Current Workflow

```
calm docify --scaffold
│
└── Generates everything at once:
├── docs/
│ ├── index.md
│ ├── nodes/*.md
│ └── relationships/*.md
├── package.json
├── sidebars.js
└── docusaurus.config.js
```

## Proposed Workflow

```
calm docify --scaffold
│
└── Phase 1: Generate content + manifest
├── docs/
│ ├── index.md
│ ├── nodes/*.md
│ └── relationships/*.md
└── index.json (NEW: site structure manifest)

calm docify --deploy (or new command)
│
└── Phase 2: Read manifest, generate deployment config
├── package.json
├── sidebars.js
└── docusaurus.config.js
```

## Example index.json Manifest

```json
{
"title": "E-Commerce System",
"version": "1.0.0",
"generatedFrom": "system.json",
"pages": [
{
"id": "index",
"path": "docs/index.md",
"label": "Overview",
"sidebar": true,
"order": 0
},
{
"id": "nodes",
"label": "Nodes",
"sidebar": true,
"order": 1,
"children": [
{ "id": "ecommerce-system", "path": "docs/nodes/ecommerce-system.md", "label": "E-Commerce System" },
{ "id": "payment-service", "path": "docs/nodes/payment-service.md", "label": "Payment Service" },
{ "id": "inventory-service", "path": "docs/nodes/inventory-service.md", "label": "Inventory Service" }
]
},
{
"id": "relationships",
"label": "Relationships",
"sidebar": true,
"order": 2,
"children": [
{ "id": "sys-composition", "path": "docs/relationships/sys-composition.md", "label": "System Composition" }
]
}
]
}
```

## User Impact

- Users can edit `index.json` to customize navigation before deploying
- Teams can version control the manifest separately from generated config
- Easier to add custom documentation pages to the sidebar
- Supports iterative workflows: regenerate content without losing sidebar customizations

## Proposed Implementation

### Phase 1: Update Scaffold Mode
1. Modify `docify --scaffold` to generate `index.json` instead of Docusaurus config
2. `index.json` describes all generated pages with metadata (path, label, order)
3. Content generation remains unchanged

### Phase 2: New Deploy Command
1. Add `calm docify --deploy` or `calm deploy` command
2. Reads `index.json` from the output directory
3. Generates `sidebars.js`, `package.json`, `docusaurus.config.js`
4. Validates that referenced pages exist

### VSCode Integration
1. Update "Create Website" command to run scaffold phase
2. Add new "Deploy Website" command for deploy phase
3. Consider a combined "Create and Deploy" option for simple workflows

## Acceptance Criteria

- [ ] `docify --scaffold` generates `index.json` manifest
- [ ] `index.json` schema is documented
- [ ] New `--deploy` flag (or command) generates Docusaurus config from manifest
- [ ] Users can manually edit `index.json` before deploy
- [ ] VSCode extension updated with separate commands
- [ ] Backward compatibility: option to run both phases together

## Open Questions

- Should `--deploy` be a flag on docify or a separate command?
- Should we support other static site generators in the future (manifest as abstraction)?
- How to handle manifest schema versioning?

## Related Files

- `shared/src/docify/docifier.ts`
- `shared/src/template/template-processor.ts`
- `shared/src/template/template-bundles/docusaurus/`
- `calm-plugins/vscode/src/commands/create-website/`