Instruct CRE skill agent to use JSON output flags on CLI commands

[thodges-gh]

Description

Updates chainlink-cre-skill so the agent requests machine-readable JSON output from CRE CLI
commands that support it, instead of parsing human-formatted text.

After auditing every cre subcommand's help output locally, exactly three commands support JSON
output, via two different flag styles:

Command	Flag
cre templates list	--json (boolean)
cre workflow list	--output json (string)
cre workflow supported-chains	--output json (string)

Changes (chainlink-cre-skill, version 0.0.12 → 0.0.13):

• references/cli-reference.md
  • Added a JSON-output rule to the "Non-Interactive Usage" section listing all three commands
    with their exact (differing) flag styles, and warning not to pass --json to commands that
    don't support it.
  • Added --output json documentation and an agent example to cre workflow list.
  • Documented the previously-missing cre workflow supported-chains command, including its
    --output json flag.
  • Added a new Templates Commands section documenting cre templates list (with --json),
    cre templates add, and cre templates remove, which were not previously documented.
• references/project-scaffolding.md
  • Updated the cre templates list reference to instruct the agent to add --json for
    machine-readable output.

Justification

The original skill referenced cre templates list without telling the agent it could emit JSON,
and didn't document cre workflow supported-chains or the JSON capabilities of cre workflow list at all. Without this guidance, the agent scrapes human-formatted tables, which is brittle
and error-prone. Pointing it at the JSON flags makes parsing reliable. Documenting the two
distinct flag styles (--json vs --output json) prevents the agent from passing --json to
commands that would reject it.

[github-actions]

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