Brew bundle reports `Upgrading X has failed!` after installing X

Symptom: bootstrap.sh upgrade pours and links a formula successfully, then reports Upgrading <formula> has failed!. Nearby errors name a vanished file in ~/.cache/Homebrew/downloads/, such as No such file or directory @ dir_s_rmdir - ...bottle_manifest.json. Several unrelated formulae can fail this way in one run.

Root cause: Homebrew Bundle defaults to as many as four package workers. Those workers launch separate brew install or brew upgrade processes that share one download cache and run install cleanup against it. One worker can remove a cache entry after another has inspected it, turning successful installs into nonzero exits. Homebrew tracks the broader parallel-worker race as Homebrew/brew#23328; the Homebrew manpage documents the auto job default and the sequential override.

Confirm after the original bootstrap process has exited:

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formula=tree
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brew list --versions "$formula"
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brew outdated --formula "$formula"
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brew linkage --test "$formula"

If the new version is listed, brew outdated prints nothing, and linkage passes, the install succeeded and only its cleanup path failed.

Graphviz has a second version of this symptom. Netpbm fetches its source and manual from Subversion. Bundle can queue those SVN fetches before it finishes installing Graphviz’s Subversion dependency, record You must: brew install svn, then install Subversion, retry both checkouts, and successfully build Netpbm and Graphviz. The early fetch result still makes Bundle print Upgrading graphviz has failed! after the successful install.

Fix: update the checkout and rerun bootstrap.sh upgrade. The shared installer environment now disables Bundle package jobs; downloads and each source build can still run concurrently, but package installs and cleanup are serialized. On Linux it also installs a working Subversion before a Brewfile containing Graphviz, then runs brew bundle check after any nonzero Bundle exit. If that check passes, it retries Bundle once and reports recovery only when the clean retry exits zero. Manual one-off:

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brew bundle install --jobs=1 --file="$HOME/dotfiles/packages/Brewfile"

Do not start the retry while the first bootstrap is still running.