Refresh skills and operator guides for 0.13

[aaltshuler]

Refresh the OmniGraph skill and operator guides for the released 0.13 workflows. Replace accumulated restart workarounds, removed HTTP routes/flags, and duplicate instructions with current live deployment, exact-receipt, policy/provider, and graph lifecycle guidance.

Keep all 13 skill reference filenames stable for the MCP bundle. This removes roughly 1,100 net lines while correcting policy-update, embedding-provider, and served-plan documentation.

Validation: skill validator, documentation checker (213 Markdown files), agent-guide links, typos, and diff whitespace all pass. No engine behavior changes.

[aaltshuler]

Keeping this PR open: the current head 2990fa3 has one incomplete qualification result. Azurite Azure Integration exceeded its 90-minute job limit and was cancelled while compiling. Tests that had executed passed, but the remaining Azure qualification and final inventory check did not finish.

The other required checks completed successfully. This is a CI completion blocker, not evidence of a failing test assertion. Complete the Azure job before merging; do not waive the gate. No rerun or workflow change was made as part of this issue-cleanup pass.