fix: report callers/callees/query truncation (#1674)

[colbymchenry]

Summary

• Lands the verified fix from fix: report CLI result truncation #1647 onto current main (that PR is conflicted on CHANGELOG.md after fix(extraction): index CommonJS export assignments as functions #1771).
• codegraph callers / callees human output shows N of M plus a widening hint; JSON includes total, limit, truncated.
• codegraph query keeps bare-array --json and reports truncation on stderr (human on stdout).
• MCP codegraph_callers / codegraph_callees answers say when the default limit cut the list (Showing N of M / … +N more).
• codegraph node already had +N more on its caller trail; unchanged.

Fixes #1674. Also addresses #1639.

Credit: @danusha2345 via #1647.

Test plan

• Reproduced silent truncation on Linux (mcp-callers-truncation 3 fail before fix)
• npx vitest run __tests__/mcp-callers-truncation.test.ts — 5 pass
• npx tsc + npx vitest run __tests__/cli-truncation.test.ts — 3 pass