feat: refactor encoderfile core -> encoderfile

[besaleli]

Description

This PR merges encoderfile-core into encoderfile, as discussed in #215.

Changes

• Moved all functionality from encoderfile-core into the main encoderfile crate
• Feature-gated the build CLI and related dependencies
• Removed the standalone encoderfile-core crate
• Updated and simplified GitHub workflows to reflect the new crate layout

Additionally:

• Switched from deprecated instrumentation mode to simulation mode as described in Run benchmarks on simulation instead of instrumentation #191
• Commented out cargo caching for ci workflow to avoid out-of-storage errors in gh workflows

Rationale

The original separation existed to support on-the-fly Rust project generation and compilation during encoderfile builds. Since encoderfile builds are now pure packaging steps over prebuilt artifacts, this split no longer provides meaningful benefits and adds unnecessary complexity.

Merging the crates improves symmetry between library and CLI use cases, reduces maintenance overhead, and simplifies the build and release pipeline.

This PR is not a final refactor of encoderfile and more breaking changes will be coming soon.

[codspeed-hq]

CodSpeed Performance Report

Merging this PR will degrade performance by 24.3%

_{Comparing 215-exploratory-refactor-encoderfile_core---encoderfile (ce7dd3e) with main (89ae444)}

Summary

⚡ 1 improved benchmark
❌ 3 (👁 3) regressed benchmarks
✅ 16 untouched benchmarks
⏩ 20 skipped benchmarks¹

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
👁	bench_tok_cls_softmax[(16, 16, 2)]	149.2 µs	184 µs	-18.91%
⚡	sequence_classification_postprocess[16]	33.6 µs	30.5 µs	+10.24%
👁	bench_tok_cls_softmax[(128, 256, 32)]	27.9 ms	35.7 ms	-21.65%
👁	bench_tok_cls_softmax[(32, 128, 8)]	1.4 ms	1.8 ms	-24.3%

Footnotes

1. 20 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

[codecov-commenter]

Codecov Report

❌ Patch coverage is 36.00000% with 16 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
encoderfile/src/build_cli/transforms/mod.rs	0.00%	10 Missing ⚠️
encoderfile/src/build_cli/cli/build.rs	0.00%	3 Missing ⚠️
encoderfile/bin/encoderfile.rs	0.00%	1 Missing ⚠️
encoderfile/src/build_cli/cli/mod.rs	0.00%	1 Missing ⚠️
encoderfile/src/build_cli/config.rs	0.00%	1 Missing ⚠️

Files with missing lines	Coverage Δ
encoderfile-runtime/src/main.rs	0.00% <ø> (ø)
...le/bin/utils/generate_encoderfile_config_schema.rs	0.00% <ø> (ø)
encoderfile/src/assets.rs	0.00% <ø> (ø)
encoderfile/src/build_cli/base_binary/mod.rs	43.43% <ø> (ø)
...coderfile/src/build_cli/base_binary/target_spec.rs	31.70% <ø> (ø)
encoderfile/src/build_cli/cache.rs	0.00% <ø> (ø)
encoderfile/src/build_cli/cli/runtime.rs	0.00% <ø> (ø)
encoderfile/src/build_cli/model.rs	97.61% <ø> (ø)
encoderfile/src/build_cli/terminal.rs	0.00% <ø> (ø)
encoderfile/src/build_cli/tokenizer.rs	77.63% <ø> (ø)
... and 62 more

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