Update from code changes: sync MCP docs with 35-tool registry

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Summary

Sweep the MCP documentation so it matches the consolidated 35-tool registry: the breadbox:// resources surface is retired, write tools have been folded together, and the operating-guidance docs are now served by a get_reference tool.

Changes

• mcp/overview.mdx — replaced the nine-row resources table with the orientation-reads tool list (get_overview, list_accounts, list_categories, …) and a get_reference(kind=…) table for the guidance docs; tool count corrected to 35.
• mcp/tools.mdx — folded the standalone count_transactions section into a query_transactions(count_only=true) note; rewrote the Series table to the new five-tool surface (list_series, get_series, assign_series, update_series, unlink_series_transactions) and removed the retired set_series_type, add/remove_series_tag, review_series, explain_series_candidates, rekey_series, split_series.
• mcp/reference/overview.mdx — dropped the Resources section and replaced it with a migration table mapping each old breadbox:// URI to its new tool; documented get_reference and its four kinds; renamed the overview shape heading; noted the registry is now 35 tools, 0 resources.
• mcp/reference/transactions.mdx — added the count_only and flagged parameters on query_transactions; replaced the count_transactions section with a query_transactions(count_only=true) note.
• mcp/reference/transactions-write.mdx — added reset_category and flagged parameters on the update_transactions operation shape; called out that the retired per-row tools (categorize_transaction, batch_categorize_transactions, reset_transaction_category, bulk_recategorize, flag_transaction, unflag_transaction) all fold into update_transactions; added a flagging example.
• mcp/reference/rules-write.mdx — rewrote create_transaction_rule to take a rules array of 1–100 specs; removed the standalone batch_create_rules section.
• mcp/reference/rules.mdx, mcp/reference/categorization.mdx, mcp/reference/conventions.mdx, mcp/reference/reports.mdx — scrubbed stale references to count_transactions, batch_create_rules, and breadbox://report-format.
• guides/*, transactions/* — replaced count_transactions(...) call sites with query_transactions(..., count_only=true); refreshed the agent-facing Series bullets in tracking-subscriptions.mdx.

Context

Reflects the consolidated MCP surface shipped in canalesb93/breadbox#1872.

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