docs: reorganize developer documentation

crates/tools/README.md

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+# tools
+
+## Role
+
+`tools` implements built-in tools and shared tool execution helpers used by Pods.
+
+## Boundaries
+
+Owns:
+
+- built-in filesystem, web, memory, and Pod-management tool implementations where applicable
+- bounded tool output formatting
+- scope-aware file operation helpers
+- tool-facing diagnostics suitable for history/model consumption
+
+Does not own:
+
+- manifest permission policy definition (`manifest`)
+- Worker tool-loop semantics (`llm-worker`)
+- Pod lifecycle decisions (`pod`)
+- UI presentation (`tui`)
+
+## Design notes
+
+A tool implementation must assume model input is untrusted. Permission policy, scope checks, output bounding, and redaction are part of the safety boundary, not optional UI behavior.
+
+## See also
+
+- [`../../docs/design/tool-permissions-scope.md`](../../docs/design/tool-permissions-scope.md)
+- [`../../docs/design/memory-knowledge.md`](../../docs/design/memory-knowledge.md)