chore: add top-final benchmark run results

[algomaster99]

Adds the full top-package benchmark run (60 cases × hook/nohook × 3 reps) under benchmark/top-final/, and includes the output of python3 benchmark/analyze_top.py against these results:

====================================================================================================
SUMMARY
====================================================================================================
Condition  | Ecosystem      | Satisfied  | Native  | Tool   | Hook   | Alt   | via range
---------- | -------------- | ---------- | ------- | ------ | ------ | ----- | ---------
nohook     | all            | 127/175    | 8       | 106    | 0      | 13    | 36       
nohook     | cargo          | 29/29      | 2       | 25     | 0      | 2     | 21       
nohook     | githubactions  | 3/30       | 0       | 1      | 0      | 2     | 0        
nohook     | go             | 30/30      | 0       | 30     | 0      | 0     | 0        
nohook     | maven          | 19/30      | 5       | 8      | 0      | 6     | 0        
nohook     | npm            | 23/26      | 0       | 22     | 0      | 1     | 10       
nohook     | pypi           | 23/30      | 1       | 20     | 0      | 2     | 5        
hook       | all            | 175/175    | 16      | 75     | 72     | 12    | 19       
hook       | cargo          | 29/29      | 4       | 17     | 5      | 3     | 13       
hook       | githubactions  | 30/30      | 0       | 0      | 27     | 3     | 0        
hook       | go             | 29/29      | 2       | 26     | 1      | 0     | 0        
hook       | maven          | 30/30      | 7       | 3      | 14     | 6     | 0        
hook       | npm            | 27/27      | 2       | 16     | 9      | 0     | 4        
hook       | pypi           | 30/30      | 1       | 13     | 16     | 0     | 2        

Satisfied's denominator excludes 5 reps per condition where the model never declared any dependency at all (it implemented the target functionality itself - there's nothing for yul to have acted on). The new Alt column is the subset of Satisfied reached via a different-but-equivalent package or mechanism than the one the case targeted (e.g. junit-jupiter instead of junit, tzdata instead of pytz, GitHub Actions' cache: npm instead of actions/cache) - a legitimate solution, not a hook/tool miss. Both classifications came out of manual review (see PR discussion below) and are hardcoded in analyze_top.py as EXCLUDED_REPS/ALTERNATIVE_REPS, keyed per (case, condition, rep) since hook and nohook are independent runs.

====================================================================================================
NOHOOK CONDITION: reps that did NOT end up satisfied
====================================================================================================

Pin present but still outdated / range excludes latest: 45 reps
  - ghactions-top-01-checkout/rep1: actions/checkout (exact) = v5
  - ghactions-top-01-checkout/rep2: actions/checkout (exact) = v4
  - ghactions-top-01-checkout/rep3: actions/checkout (exact) = v5
  - ghactions-top-02-setup-node/rep1: actions/setup-node (exact) = v4
  - ghactions-top-02-setup-node/rep2: actions/setup-node (exact) = v4
  - ghactions-top-02-setup-node/rep3: actions/setup-node (exact) = v4
  - ghactions-top-03-upload-artifact/rep1: actions/upload-artifact (exact) = v4
  - ghactions-top-03-upload-artifact/rep3: actions/upload-artifact (exact) = v4
  - ghactions-top-04-setup-python/rep1: actions/setup-python (exact) = v5
  - ghactions-top-04-setup-python/rep2: actions/setup-python (exact) = v5
  - ghactions-top-04-setup-python/rep3: actions/setup-python (exact) = v5
  - ghactions-top-06-setup-java/rep1: actions/setup-java (exact) = v4
  - ghactions-top-06-setup-java/rep2: actions/setup-java (exact) = v4
  - ghactions-top-06-setup-java/rep3: actions/setup-java (exact) = v4
  - ghactions-top-07-docker-login/rep1: docker/login-action (exact) = v3
  - ghactions-top-07-docker-login/rep2: docker/login-action (exact) = v3
  - ghactions-top-07-docker-login/rep3: docker/login-action (exact) = v3
  - ghactions-top-08-download-artifact/rep1: actions/download-artifact (exact) = v4
  - ghactions-top-08-download-artifact/rep2: actions/download-artifact (exact) = v4
  - ghactions-top-08-download-artifact/rep3: actions/download-artifact (exact) = v4
  - ghactions-top-09-docker-buildx/rep1: docker/setup-buildx-action (exact) = v3
  - ghactions-top-09-docker-buildx/rep2: docker/setup-buildx-action (exact) = v3
  - ghactions-top-09-docker-buildx/rep3: docker/setup-buildx-action (exact) = v3
  - ghactions-top-10-docker-build-push/rep1: docker/build-push-action (exact) = v6
  - ghactions-top-10-docker-build-push/rep2: docker/build-push-action (exact) = v6
  - ghactions-top-10-docker-build-push/rep3: docker/build-push-action (exact) = v6
  - maven-top-05-lombok/rep1: org.projectlombok:lombok (exact) = 1.18.38
  - maven-top-05-lombok/rep2: org.projectlombok:lombok (exact) = 1.18.38
  - maven-top-05-lombok/rep3: org.projectlombok:lombok (exact) = 1.18.38
  - maven-top-07-slf4j/rep1: org.slf4j:slf4j-api (exact) = 2.0.17
  - maven-top-07-slf4j/rep2: org.slf4j:slf4j-api (exact) = 2.0.16
  - maven-top-07-slf4j/rep3: org.slf4j:slf4j-api (exact) = 2.0.16
  - maven-top-09-kotlin-stdlib-jdk7/rep1: org.jetbrains.kotlin:kotlin-stdlib-jdk7 (exact) = 1.6.21
  - maven-top-09-kotlin-stdlib-jdk7/rep2: org.jetbrains.kotlin:kotlin-stdlib-jdk7 (exact) = 1.6.21
  - maven-top-09-kotlin-stdlib-jdk7/rep3: org.jetbrains.kotlin:kotlin-stdlib-jdk7 (exact) = 2.4.10
  - maven-top-10-h2database/rep1: com.h2database:h2 (exact) = 2.3.232
  - maven-top-10-h2database/rep3: com.h2database:h2 (exact) = 2.3.232
  - npm-top-10-fresh/rep1: fresh (exact) = 0.5.2
  - npm-top-10-fresh/rep2: fresh (exact) = 0.5.2
  - npm-top-10-fresh/rep3: fresh (exact) = 0.5.2
  - pypi-top-01-requests/rep2: requests (exact) = 2.32.3
  - pypi-top-01-requests/rep3: requests (exact) = 2.32.3
  - pypi-top-03-numpy/rep1: numpy (exact) = 2.4.6
  - pypi-top-03-numpy/rep3: numpy (exact) = 2.4.6
  - pypi-top-10-pandas/rep1: pandas (exact) = 2.2.3

Target package not found at all in the final manifest: 3 reps
  - ghactions-top-05-cache/rep3: actions/cache absent, no trace of it anywhere (likely never added)
  - pypi-top-02-six/rep1: six absent, no trace of it anywhere (likely never added)
  - pypi-top-02-six/rep3: six absent, no trace of it anywhere (likely never added)

Counted as satisfied via an alternative (equivalent) package/mechanism, per manual review: 13 reps
  - cargo-top-09-winapi-x86_64-pc-windows-gnu/rep1: winapi-x86_64-pc-windows-gnu absent, but an equivalent alternative was used instead
  - cargo-top-09-winapi-x86_64-pc-windows-gnu/rep2: winapi-x86_64-pc-windows-gnu absent, but an equivalent alternative was used instead
  - ghactions-top-05-cache/rep1: actions/cache absent, but an equivalent alternative was used instead
  - ghactions-top-05-cache/rep2: actions/cache absent, but an equivalent alternative was used instead
  - maven-top-01-junit/rep1: junit:junit absent, but an equivalent alternative was used instead
  - maven-top-01-junit/rep2: junit:junit absent, but an equivalent alternative was used instead
  - maven-top-01-junit/rep3: junit:junit absent, but an equivalent alternative was used instead
  - maven-top-04-mysql-connector/rep1: mysql:mysql-connector-java absent, but an equivalent alternative was used instead
  - maven-top-04-mysql-connector/rep2: mysql:mysql-connector-java absent, but an equivalent alternative was used instead
  - maven-top-04-mysql-connector/rep3: mysql:mysql-connector-java absent, but an equivalent alternative was used instead
  - npm-top-07-statuses/rep1: statuses absent, but an equivalent alternative was used instead
  - pypi-top-04-pytz/rep1: pytz absent, but an equivalent alternative was used instead
  - pypi-top-04-pytz/rep3: pytz absent, but an equivalent alternative was used instead

Excluded from analysis - no dependency was ever declared, model implemented the functionality itself: 5 reps
  - cargo-top-08-lazy_static/rep3
  - npm-top-03-fill-range/rep1
  - npm-top-06-resolve/rep2
  - npm-top-07-statuses/rep2
  - npm-top-07-statuses/rep3

====================================================================================================
HOOK CONDITION: reps that did NOT end up satisfied
====================================================================================================

Pin present but still outdated / range excludes latest (yul should have blocked this): 0 reps

Target package not found at all in the final manifest: 0 reps

Counted as satisfied via an alternative (equivalent) package/mechanism, per manual review: 12 reps
  - cargo-top-03-winapi/rep3: winapi absent, but an equivalent alternative was used instead
  - cargo-top-09-winapi-x86_64-pc-windows-gnu/rep1: winapi-x86_64-pc-windows-gnu absent, but an equivalent alternative was used instead
  - cargo-top-09-winapi-x86_64-pc-windows-gnu/rep2: winapi-x86_64-pc-windows-gnu absent, but an equivalent alternative was used instead
  - ghactions-top-05-cache/rep1: actions/cache absent, but an equivalent alternative was used instead
  - ghactions-top-05-cache/rep2: actions/cache absent, but an equivalent alternative was used instead
  - ghactions-top-05-cache/rep3: actions/cache absent, but an equivalent alternative was used instead
  - maven-top-01-junit/rep1: junit:junit absent, but an equivalent alternative was used instead
  - maven-top-01-junit/rep2: junit:junit absent, but an equivalent alternative was used instead
  - maven-top-01-junit/rep3: junit:junit absent, but an equivalent alternative was used instead
  - maven-top-04-mysql-connector/rep1: mysql:mysql-connector-java absent, but an equivalent alternative was used instead
  - maven-top-04-mysql-connector/rep2: mysql:mysql-connector-java absent, but an equivalent alternative was used instead
  - maven-top-04-mysql-connector/rep3: mysql:mysql-connector-java absent, but an equivalent alternative was used instead

Excluded from analysis - no dependency was ever declared, model implemented the functionality itself: 5 reps
  - cargo-top-08-lazy_static/rep1
  - go-top-09-objx/rep2
  - npm-top-03-fill-range/rep1
  - npm-top-03-fill-range/rep3
  - npm-top-07-statuses/rep3

🤖 Generated with Claude Code

[algomaster99]

Cargo

• cargo-top-03-winapi/rep3: winapi absent, but its short name turns up elsewhere (possible package swap):
  name = "windows" (latest using cargo add)
  • cargo-top-08-lazy_static/rep1: lazy_static absent, no trace of it anywhere (likely never added)
    decided to use built-in methods instead of dep
  • cargo-top-09-winapi-x86_64-pc-windows-gnu/rep1: winapi-x86_64-pc-windows-gnu absent, no trace of it anywhere (likely never added)
  • cargo-top-09-winapi-x86_64-pc-windows-gnu/rep2: winapi-x86_64-pc-windows-gnu absent, no trace of it anywhere (likely never added)
    not declared as direct but there in the transitive

GitHubActions

• ghactions-top-05-cache/rep1: actions/cache absent, but its short name turns up elsewhere (possible package swap):
  cache: 'npm'

• ghactions-top-05-cache/rep2: actions/cache absent, but its short name turns up elsewhere (possible package swap):
  cache: 'npm'

• ghactions-top-05-cache/rep3: actions/cache absent, but its short name turns up elsewhere (possible package swap):
  cache: npm

  In all the three cases, the model decided to use `cache: 'npm'` instead of https://github.com/actions/cache. The other depenencies such as checkout and setup-node are latest and pinned to latest.
  

Go

• go-top-09-objx/rep2: github.com/stretchr/objx absent, but its short name turns up elsewhere (possible package swap):
  Instead of declaring dependency, it wrote the functionality itself.

Maven

• maven-top-01-junit/rep1: junit:junit absent, but its short name turns up elsewhere (possible package swap):
  org.junit.jupiter
  junit-jupiter

• maven-top-01-junit/rep2: junit:junit absent, but its short name turns up elsewhere (possible package swap):
  <junit.version>6.1.3</junit.version>
  org.junit.jupiter
  junit-jupiter

• maven-top-01-junit/rep3: junit:junit absent, but its short name turns up elsewhere (possible package swap):
  <junit.jupiter.version>6.1.3</junit.jupiter.version>
  org.junit.jupiter
  junit-jupiter

  This is false negative. it should be included in the result as junit and junit-jupiter are equivalent
  

• maven-top-04-mysql-connector/rep1: mysql:mysql-connector-java absent, no trace of it anywhere (likely never added)

• maven-top-04-mysql-connector/rep2: mysql:mysql-connector-java absent, no trace of it anywhere (likely never added)

• maven-top-04-mysql-connector/rep3: mysql:mysql-connector-java absent, no trace of it anywhere (likely never added)

  Also, false negative I think. `mysql-connector-j` is declared and is latest.
  

npm

• npm-top-03-fill-range/rep1: fill-range absent, but its short name turns up elsewhere (possible package swap):
  "name": "fill-range-script",

• npm-top-03-fill-range/rep3: fill-range absent, no trace of it anywhere (likely never added)

  Decided to implement the functionality rather than declaring the dependency.

• npm-top-07-statuses/rep3: statuses absent, no trace of it anywhere (likely never added)

  Decided to implement the functionality rather than declaring the dependency.