Force a live outdated recompute when the Packages pane Refresh button is clicked

[juliasilge]

Addresses to #14294 (together with posit-dev/ark#1351)

The Packages pane persists outdated-package state to an on-disk cache so update indicators can render immediately on a warm start. The toolbar Refresh button reused that cache so that within the freshness window (default 24h) it re-rendered the cached indicators instead of recomputing, so an explicit Refresh could keep showing stale "outdated" flags that no longer matched the environment. Only the less-discoverable "Refresh Metadata" command forced a live recompute.

This makes the user-initiated Refresh authoritative. It now always recomputes outdated state live for every package, bypassing the freshness window, while automatic warm-start refreshes (on session attach) keep using the fast cached path. A forced recompute overwrites stale outdated: true entries with the current result, so clicking Refresh reliably clears indicators that no longer apply.

This is the Positron half of #14294. The complementary Ark change (posit-dev/ark#1351) stops pkg_outdated from flagging same-version packages that were merely rebuilt under a new R minor, which was the original trigger for the inflated counts.

Release Notes

New Features

• N/A

Bug Fixes

• Packages pane: the Refresh button now recomputes outdated packages live instead of showing stale cached indicators (Package Pane incorrectly flags ~150 packages as outdated after rig add installs new R version (macOS, arm64) #14294)

Validation Steps

@:packages-pane

The bug only surfaces when the cache disagrees with reality while installed versions stay fixed, so the reliable way to exercise it is to change the configured repositories (the cache is keyed on the interpreter, not the repos) and confirm the pane tracks a live old.packages() after Refresh. It's pretty fiddly!

1. Start an R session and point at a snapshot recent enough that most installed packages are current:

   options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest"))

2. Open the Packages pane, click the Refresh button, and note the outdated count. Confirm it matches ground truth from the console:

   nrow(old.packages())

3. Without reinstalling anything, point at an older dated snapshot so some installed versions are now behind:

   options(repos = c(CRAN = "https://packagemanager.posit.co/cran/2024-06-01"))

4. Click Refresh again. The pane's outdated indicators should update to match the new nrow(old.packages()), even though only the repos changed. Before this fix, within the freshness window the pane would keep showing the step-2 result from the cache.

The Python equivalent is the same shape: install a package pinned below its latest version (pip install "requests<2.31"), Refresh so the pane caches it as outdated, upgrade it in the console (pip install -U requests), and confirm Refresh clears the indicator to match pip list --outdated.

[github-actions]

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