Fix dependabot security alerts across workspace

[mishushakov]

Summary

Resolves all 31 open dependabot alerts across the repo's npm and pip manifests.

• pnpm-lock.yaml: added pnpm.overrides for postcss, vite, yaml, flatted, minimatch (3.x and 9.x), and rollup
• template/poetry.lock: bumped python-dotenv to 1.2.2 and pygments to 2.20.0
• examples/basic-python: bumped e2b-desktop to ^2.3.1 (pulls pillow 12.2.0) and python-dotenv to ^1.2.2
• packages/python-sdk: bumped dev pytest to ^9.0.3 (pulls pygments 2.20.0)
• examples/basic-javascript: bumped electron to ^39.8.5 (resolves 17 electron CVEs)

Test plan

• CI passes
• pnpm install, pnpm build (js-sdk), and pnpm lint succeed locally
• Dependabot alerts close after merge

🤖 Generated with Claude Code

[cursor]

PR Summary

Medium Risk
Mostly dependency/lockfile upgrades, but includes a major electron bump and workspace-wide pnpm.overrides, which could introduce runtime/build incompatibilities.

Overview
Resolves dependency security alerts by upgrading example and SDK dependencies and regenerating lockfiles.

Notably bumps examples/basic-javascript from electron ^35 to ^39, upgrades examples/basic-python to e2b-desktop ^2.3.1 and python-dotenv ^1.2.2 (pulling newer e2b, pillow, and new transitive deps), and updates packages/python-sdk dev tooling (pytest to ^9.0.3).

Adds root-level pnpm.overrides (mirrored into pnpm-lock.yaml) to force patched versions of postcss, vite, yaml, flatted, minimatch (3.x/9.x), and rollup across the workspace.

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