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fix(cli, docs): Refactor and enhance approximation modules and CLI support - #380
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Add project scaffolding, pinned dependency builds, on-demand rebuilds, compiled-output resolution, diagnostics, and documentation for custom dataflow approximations.
Three defects found by the model in formal/Opentaint/Cli/Internal/Approximation, each with the test the proof predicts. A directory counted as compiled classes as soon as a .class file existed anywhere below it. That is a test of the subtree, not a classification of the directory: a tree holding both a model project and compiled classes collapsed to one classpath root, the project was never compiled, and the scan ran without its models and reported nothing about it. Classify only when nothing below still needs building, and compute both facts in one walk rather than two (Resolve.fixed_loses_nothing, Resolve.shipped_loses_a_project, Resolve.fused_resolves_identically). A directory holding compiled classes of its own next to a project has no valid classification at all, so report it by name instead of dropping either side (Resolve.ambiguous_tree_drops_a_class). Builds staged in a directory named after the output alone, so two builders of one project shared it: one could delete the other's classes, contribute to them, and publish the mixture under a stamp recording it as up to date. Stage under a path carrying the builder's identity, and rename the previous output aside rather than deleting it, so a reader sees the old output, the new one, or nothing (Build.raceA_output_is_not_sound, Build.publishedOutputIsSound). The rebuild stamp digested the model project but not the compiler that reads it, so an upgraded CLI kept serving models compiled by the previous one. Carry the autobuilder's identity in the stamp (Stamp.shipped_stamp_serves_a_stale_output, Stamp.full_stamp_covers).
The remaining findings from the stack review. Two resolved class directories could offer the same class with different content, and nothing says which one an analysis reads, so the finding set depended on a choice the CLI never made. ResolveAll resolves every --dataflow-approximations path together, passes each directory once, and rejects a classpath whose directories disagree about a class they share. Identical copies are the ordinary result of overlapping paths and stay free (Resolve.agreement_pins_the_choice, Resolve.identical_roots_agree, Resolve.duplicate_root_is_harmless). Staging directories now live in a .opentaint-staging directory beside the output, on the skip list, so that what a killed build leaves behind is never resolved as compiled models — half-built classes applied to a scan is the same silent-loss shape as the rest of this review. The next build reclaims them, but only once the owning process is gone, so a build in progress is never disturbed; sweeping cannot reach the published output at all (Build.sweep_leaves_the_output). A build output recorded the absolute path of the project it came from, so it meant nothing on another machine. Record it relative to the output. A javac error count is a trailer for the diagnostics above it, not a diagnostic: a line that merely reads like one no longer stands in for the compiler output. Also drop a redundant sort of os.ReadDir output and a deferred close inside a loop.
Take the approximation project's pins from the batch's test project, drop rationale and CLI internals that duplicate existing instructions, and keep compilation feedback in the approximation test run.
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