docs: mirror canonical documentation behavior to docs-web

[numnx]

This PR removes stale references to deprecated manage_code_ux usages and .jules-subagents directory configuration in the web documentation (docs-web/) to match the canonical state in docs/. It updates tool names (e.g., manage_settings, manage_projects) and marks legacy .jules-subagents fallback instructions as deprecated. All updates correspond to current behavioral reality.

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PR created automatically by Jules for task 4172705759099593598 started by @numnx

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