[codex] chore: batch dependency maintenance for v0.5.3

[andresvio]

Summary

• Batch Dependabot PRs chore(deps): Bump github.com/mark3labs/mcp-go from 0.46.0 to 0.54.1 in /knowledgeprim in the all group across 1 directory #30, chore(deps): Bump github.com/mark3labs/mcp-go from 0.46.0 to 0.54.1 in /queueprim in the all group across 1 directory #31, chore(deps): Bump github.com/mark3labs/mcp-go from 0.46.0 to 0.54.1 in /stateprim in the all group across 1 directory #32, chore(deps): Bump modernc.org/sqlite from 1.48.2 to 1.51.0 in /primkit in the all group across 1 directory #33, and chore(deps): Bump github.com/mark3labs/mcp-go from 0.46.0 to 0.54.1 in /taskprim in the all group across 1 directory #34 into one maintenance PR.
• Update github.com/mark3labs/mcp-go from v0.46.0 to v0.54.1 across taskprim, stateprim, knowledgeprim, and queueprim.
• Update modernc.org/sqlite from v1.48.2 to v1.51.0 in the shared primkit module.
• Add a v0.5.3 changelog entry and backfill the missing v0.5.2 changelog entry.
• Run the repo make tidy cleanup so primitive modules do not retain workspace-local github.com/propifly/primkit/primkit pseudo-version requirements.

Validation

• PATH="/Users/avergara/go/bin:$PATH" make all
• Built-binary dogfood: task create/read/done, state set/get, knowledge capture/get/search, queue enqueue/dequeue/complete using temporary SQLite DBs.
• cd knowledgeprim && go test -fuzz=FuzzSanitizeFTS5Query -fuzztime=30s ./internal/store/
• PATH="/Users/avergara/go/bin:$PATH" GOTOOLCHAIN=go1.26.4 govulncheck ./... across primkit, taskprim, stateprim, knowledgeprim, and queueprim.

Merge Notes

This should be squash-merged as one dependency-maintenance change. After it lands, the original Dependabot PRs should become redundant; close any that GitHub/Dependabot does not auto-close.