fix(native-sidecar): preserve Python edits to API-seeded files

[ankssjain]

• Fixes Python edits to filesystem.writeFile-created files are reverted by shadow reconciliation #2022: preserve Python edits to API-seeded files across shadow reconciliation, including overwrites, read-modify-write, and temporary-file replacement.
• Refresh existing root shadows with the bytes already supplied to the Python VFS write handler; keep guest-only files kernel-owned and remove obsolete destination inventory after kernel-only replacements.
• Resolve symlink targets before mirroring, exclude non-root mounts, and avoid requiring an extra guest fs.stat permission for trusted post-write bookkeeping.
• Add regressions for repeated API reads, subsequent Python executions, symlinks, mounted files, and guest-only directories. Both new tests pass as root and as UID 1000; 13 additional focused existing regressions pass. The overwrite regression fails on unpatched upstream.
• Validation notes and existing baseline failures are recorded on Python edits to filesystem.writeFile-created files are reverted by shadow reconciliation #2022. Tested native source at c3698e6 with a bridge built from that checkout; the existing JavaScript/shell regression used published 0.2.22 WASM command assets. No generated assets or version changes are included.
• Does not fix shell/WASM shadow writes (Native root filesystem returns stale data after a guest process overwrites an API-created file #1901), nested Python scheduling (Python launched through guest shell stalls on queued filesystem RPCs #2012), or separate Python empty-write/truncate/append-position behavior.

[the-company-company]

🟠 1 medium-severity finding

_{Reviewed commit f1e1bac.}

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🟠 Medium · Mirroring rejects writes to read-only shadow files after the kernel write succeeds

kernel.write_file has already accepted and committed the Python write, but fs::write re-applies the host sidecar user's DAC permissions to the shadow copy. Because the sidecar is intentionally unprivileged, an API-seeded file whose guest mode is 0444/0000 makes this return EACCES; the RPC reports failure after mutating the kernel and leaves stale shadow bytes that reconciliation can restore. Temporarily add owner-write permission to an existing regular shadow file, write it, and restore the guest mode (including on the error path), or use an equivalent sidecar-owned write helper.

Original location: "crates/native-sidecar/src/filesystem.rs":5130 (new side, not submitted inline).