Fixes #336

Problem

BuiltinToolStore.Seed() performs a reconcile DELETE that removes all rows not in the provided list:

DELETE FROM builtin_tools WHERE name != ALL($1)

When a fork calls Seed() twice — once for 28 upstream tools, then again for 2 fork-local tools — the second call's DELETE wipes all 28 upstream tools. Only the 2 fork tools remain visible.

Fix

Add Upsert() method that performs the same INSERT ON CONFLICT DO UPDATE as Seed() but skips the reconcile DELETE. Fork-specific seed functions use Upsert() to additively register tools.

// Seed: full reconciliation — for upstream canonical tool set
Seed(ctx, upstreamTools)   // INSERT 28 tools, DELETE stale

// Upsert: additive — for fork-specific tools
Upsert(ctx, forkTools)     // INSERT 2 tools, no DELETE

Behavior comparison

Both methods preserve user-customized enabled and settings values — the ON CONFLICT clause only overwrites settings when the existing value is {} or null.

Changes

Verification

go build ./...                   # ✅ PG build
go build -tags sqliteonly ./...  # ✅ SQLite build  
go vet ./...                     # ✅ Clean

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