docs: add core commands reference and simplify README CLI section

[mnriem]

Adds a core commands reference page and simplifies the README by moving CLI reference details to the docs site.

Changes

• New docs/reference/core.md — reference for init (active options only, no deprecated flags), check, and version commands with copilot as the consistent example
• docs/toc.yml — added Core Commands under Reference section
• README.md — replaced the verbose CLI Reference section (init options table with deprecated flags, 30+ per-agent examples, environment variables) with a concise list of links to the five reference docs; uses copilot as the main example throughout

Motivation

The README had accumulated a large CLI Reference section with deprecated options (--skip-tls, --debug, --github-token), legacy --ai flag examples for every agent, and content that duplicated what's now in the reference docs. Since the quickstart section already covers getting started, the CLI Reference section only needs to point users to the canonical reference documentation.

This completes the reference documentation reorganization started in #2241, #2242, #2243, and #2244.

[Copilot]

Pull request overview

Adds a new “Core Commands” reference doc and trims the README’s CLI reference section down to links to the docs site.

Changes:

• Added docs/reference/core.md documenting specify init, specify check, and specify version/--version.
• Updated docs/toc.yml to include the new Core Commands page under Reference.
• Simplified README.md by replacing the long CLI reference section with links to the docs site.

Show a summary per file

File	Description
docs/toc.yml	Adds “Core Commands” entry under the Reference section.
docs/reference/core.md	New reference page for core CLI commands and key options.
README.md	Removes verbose CLI reference and replaces with links; updates examples to use copilot.

Copilot's findings

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Comments suppressed due to low confidence (3)

README.md:523

• These detailed-process examples still document --ai, which is deprecated in the CLI and emits a warning. Consider switching this whole block to --integration ... to keep the walkthrough aligned with the current command surface.

# Force merge into a non-empty current directory
specify init . --force --ai copilot

# or
specify init --here --force --ai copilot

The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, Codex CLI, Qoder CLI, Tabnine CLI, Kiro CLI, Pi, Forge, Goose, or Mistral Vibe installed. If you do not, or you prefer to get the templates without checking for the right tools, use --ignore-agent-tools with your command:

specify init <project_name> --ai copilot --ignore-agent-tools

README.md:529

• This example uses deprecated --ai; prefer --integration copilot --ignore-agent-tools for consistency with the new reference docs and to avoid recommending a flag planned for removal.
  README.md:105
• Same issue here: this uvx ... specify init example uses deprecated --ai. Prefer --integration copilot to match the reference docs and avoid showing a flag slated for removal.

uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init . --ai copilot
# or
uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here --ai copilot

• Files reviewed: 4/4 changed files
• Comments generated: 2