refactor(search): type repository, user, org and commit search tools

[SamMorrowDrums]

Summary

Migrate exactly search_repositories, search_users, search_orgs, and search_commits to concrete typed inputs and outputs. This draft is a focused layer above #3394; native stack registration is left to the coordinator.

Why

Continue the protocol-gated typed read/search migration without changing legacy text responses or search semantics.
Fixes # N/A — migration layer above #3394, not an issue-closing change.

What changed

• Use existing NewTool[In, Out] registration and shared pagination/schema helpers, preserving legacy coercion, zero/default pagination, type qualifiers, sanitization, errors, scopes, IFC labels, and repository minimal/full output selection.
• Model full repository responses with a concrete recursive DTO and JSON-compatible custom-property union, avoiding upstream map[string]any; test upstream field coverage and absence of untyped output fields.
• Add modern (2026-07-28), legacy (2025-11-25), and unknown-protocol list/call coverage, byte-exact text assertions, success/empty/error cases, schema Resolve and actual structured output validation. Update relevant snapshots.

MCP impact

• No tool or API changes
• Tool schema or behavior changed
  Modern negotiated clients receive concrete output schemas and validated structured content. Legacy/unknown clients retain text and see neither; input schema definitions and legacy text ordering are unchanged.
• New tool added

Prompts tested (tool changes only)

• Automated MCP calls (mock GitHub API, not live prompts): search repositories/users/orgs/commits with query: "repo:owner/repo fix"; verify default and string/numeric-zero pagination and nonzero string coercion.
• Automated MCP calls with query: "type:org (location:seattle OR location:california)" verify that an existing type qualifier is not duplicated.
• Repository search with minimal_output: false/true, recursive custom properties, empty responses, and errors; user/org sparse profiles and commit metadata/IFC labels.

Security / limits

• No security or limits impact
• Auth / permissions considered
  Existing public-read and read:org scope requirements are unchanged; client/API failures remain tool errors.
• Data exposure, filtering, or token/size limits considered
  Preserve compact default responses, explicit full repository output, existing sanitization, and IFC metadata. No new fields are exposed beyond existing full output.

Tool renaming

• I am renaming tools as part of this PR (e.g. a part of a consolidation effort)
  • I have added the new tool aliases in deprecated_tool_aliases.go
• I am not renaming tools as part of this PR

Note: if you're renaming tools, you must add the tool aliases. For more information on how to do so, please refer to the official docs.

Lint & tests

• Linted locally with ./script/lint
script/lint: passed, 0 issues.
• Tested locally with ./script/test
script/test: passed (go test -race ./...); pkg/github reported ok in 140.083s.

Additional validation:

• UPDATE_TOOLSNAPS=true go test ./...: passed; pkg/github reported ok in 16.065s.
• go test ./pkg/github -run 'TestTypedAccountRepositorySearch|TestSearchRepositoryOutputCoversUpstreamFields|TestSearchPropertyValueJSONUnion|TestSearchOutputsHaveNoUntypedFields' -count=1: passed (0.343s).
• script/generate-docs: passed; reported successful updates to README and remote-server/insiders-features/feature-flags/tool-renaming docs, with no resulting documentation diff.
• git diff --check: passed.

The final required sequence was script/lint → script/test → script/generate-docs → git diff --check, all exit 0. Live E2E tests were not run (require a GitHub PAT).

Parent verification: original local/live #3394 head was 83955ca85c929687a0630503dcc061b1b9af4537; synchronized before edits to the license-bot commit a6b1d6931d0f2e20c62f6fe6b03b1416a5acc93d. That parent delta changes only three license files (3 insertions, 3 deletions). Final merge-base is exactly a6b1d6931d0f2e20c62f6fe6b03b1416a5acc93d; the only layer commit is c918f4b7b9f570f468e7b4566e2392acd2f1b44c, touching eight search implementation/test/snapshot files. License-bot commit is unchanged. Signing failed with 1Password: failed to fill whole buffer; retried using command-local git -c commit.gpgsign=false commit only.

Docs

• Not needed
  Documentation generation completed and produced no content changes.
• Updated (README / docs / examples)