agent: Address some PR feedback

[jshearer]

Description:

This addresses the remaining PR feedback from #2263

• use remove() to avoid cloning in initializes_read_schema
• simplify initial read schema discovery codepaths
• simplify setting x-complexity-limit on inferred schemas
  • Initialize shapes with default complexity limit annotation
  • Raise complexity limit to 10,000 when sourced schemas are applied in apply_sourced_schemas

Tested this locally with a hello-world and postgres connector, confirming that their behavior is expected: hello-world has x-complexity-limit: 1000 and postgres has x-complexity-limit: 10000

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This change is 

[jshearer]

@jgraettinger I put this together a while ago and finally got around to actually testing it, and in the intervening time some other changes happened to crates/control-plane-api/src/discovers/specs.rs. I believe I resolved the conflict appropriately, but I'm just pointing that out as a place I could have misunderstood things.

Edit:
Alright nevermind, there's been more drift than I thought. Taking this back to draft