M12 candidate: toolkit-owned tool modules

[roackb2]

Summary

• move coding, knowledge, external-context, internal, and shell tool implementations into toolkit-owned module folders
• remove flat compatibility re-exports and delete old duplicate toolkit assembly files
• keep default tool behavior stable while adding toolkit composition guardrails and stronger default-tool ordering coverage

Verification

• yarn vitest run src/tests/integration/core/agent-loop.test.ts src/tests/integration/tools/tools.test.ts src/tests/integration/memory/memory-integration.test.ts src/tests/unit/tools/run-shell.command.test.ts
• yarn eslint
• yarn typecheck

Candidate handoff notes

• files moved: coding-files, knowledge, external-context, internal, and shell implementations now live under src/core/tools/toolkits/*
• compatibility re-exports kept or removed: removed for coding-files, knowledge, external-context, internal, and shell paths; imports updated directly
• behavior tests added/strengthened: stable default-tool ordering plus toolkit duplicate-id and duplicate-tool-name guardrails
• duplicate/wrapper leftovers checked: searched for old flat tool paths and old shell-process/run-shell paths; no matches remain
• what became clearer: each tool family now has one production ownership location and default-tools consumes those toolkit-owned modules directly
• remaining risks/follow-up: shell policy is still implemented inside the internal run-shell module rather than a dedicated shell-policy module, which remains appropriate follow-up for a later milestone rather than this cleanup