docs: add workflows reference, reorganize into docs/reference/, and add --version flag

[mnriem]

Adds a workflows reference page, reorganizes all reference docs into docs/reference/, renames the workflow feature_name input to spec, and adds a --version flag to the root specify command.

Changes

Docs reorganization

• Move docs/integrations.md, docs/extensions.md, docs/presets.md → docs/reference/
• Update docs/toc.yml, README.md links, and docs/upgrade.md cross-reference to use reference/ paths

New workflows reference

• New docs/reference/workflows.md — command reference for all workflow CLI commands, built-in Full SDD Cycle workflow with Mermaid diagram, 10 step types, expressions, input types, state/resume, catalog management, and FAQ
• Add workflow command to the README CLI reference table with link to published docs

Workflow input rename

• Rename feature_name → spec with prompt "Describe what you want to build" in workflows/speckit/workflow.yml to match the /speckit.specify command terminology ("describe what you want to build")
• Update workflows/README.md, workflows/PUBLISHING.md, src/specify_cli/workflows/expressions.py docstring, and tests/test_workflows.py fixtures

CLI --version flag

• Add --version / -V flag to the root specify command
• New tests/test_cli_version.py with 3 tests covering long flag, short flag, and precedence over subcommands

Tests

All 1485 tests pass.

[Copilot]

Pull request overview

This PR updates Spec Kit’s documentation structure and workflow UX while adding a root specify --version flag to improve CLI ergonomics.

Changes:

• Reorganized docs reference pages under docs/reference/, updated TOC and README links, and added a new Workflows reference page.
• Renamed the Speckit workflow input from feature_name → spec across workflow YAML, docs, and tests.
• Added --version / -V to the root CLI with dedicated test coverage.

Show a summary per file

File	Description
workflows/speckit/workflow.yml	Updates required Spec Kit version and renames workflow input to spec.
workflows/README.md	Updates workflow usage examples to use spec input.
workflows/PUBLISHING.md	Updates publishing guide examples to use spec input.
tests/test_workflows.py	Updates fixtures/assertions for the renamed workflow input.
tests/test_cli_version.py	Adds tests for --version / -V behavior and precedence.
src/specify_cli/workflows/expressions.py	Updates expression docstring example to inputs.spec.
src/specify_cli/init.py	Adds root --version / -V eager option and callback.
docs/upgrade.md	Fixes link to new docs/reference/integrations.md path.
docs/toc.yml	Points reference entries to docs/reference/* and adds Workflows.
docs/reference/workflows.md	New workflows command/reference documentation.
docs/reference/presets.md	Moved/added presets reference page under docs/reference/.
docs/reference/integrations.md	Moved/added integrations reference page under docs/reference/.
docs/reference/extensions.md	Moved/added extensions reference page under docs/reference/.
README.md	Updates published docs links and adds workflow command entry/link.

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• Files reviewed: 11/14 changed files
• Comments generated: 1