docs: flatten single-file catalog dirs to docs/tool-catalog.md and docs/persistence-catalog.md
A directory holding exactly one file adds a path level for nothing; cordis-catalog/ keeps its folder because it holds two sibling pages (events.md + services.md), matching config-catalog.md which was born flat. docs/tool-catalog/tools.md -> docs/tool-catalog.md and docs/persistence-catalog/log-events.md -> docs/persistence-catalog.md; their generators' OUT paths and in-page relative links drop one directory level, and every citation repo-wide (docs, RFCs, package READMEs, generator headers) is updated. graph-atlas.md, config-catalog.md, and the doc graphs regenerate with the new paths.
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@@ -8,7 +8,7 @@ Tool registry and execution pipeline. Tool plugins register their schemas and ex
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- `ctx.tools.register(definition: ToolDefinition): () => void` Register a tool. Disposed with the calling fiber.
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- `ctx.tools.get(name: string): ToolDefinition | undefined`
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- `ctx.tools.schemas(): ToolSchema[]` Schemas of all registered tools (without the `execute` functions). The shipped tools' schemas are catalogued in [docs/tool-catalog/tools.md](../../../docs/tool-catalog/tools.md), generated by booting each tool plugin and harvesting this method (see [the tool-schema-catalog RFC](../../../docs/rfc/implemented/process/2026-07-02-tool-schema-catalog.md)).
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- `ctx.tools.schemas(): ToolSchema[]` Schemas of all registered tools (without the `execute` functions). The shipped tools' schemas are catalogued in [docs/tool-catalog.md](../../../docs/tool-catalog.md), generated by booting each tool plugin and harvesting this method (see [the tool-schema-catalog RFC](../../../docs/rfc/implemented/process/2026-07-02-tool-schema-catalog.md)).
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- `ctx.tools.execute(exec: ToolExecution): Promise<ToolExecutionResult>` Execute one tool call through the `tools/pre-execute` → dispatch → `tools/post-execute` pipeline.
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### Injected services
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