Fix bugs with workflow outputs

[bentsherman]

TODO:

• Fix output block is needed for publishing outputs from workflow #5460
• Fix Output DSL not creating parent directory.  #5465
• Fix Dynamic publish path is not resolved against output directory #5476
• Fix Bug in workflow output definitions with HTTP input file publishing #5480
• Fix outputDir can't be used as an implicit variable within a config #5543
• Update unit tests, e2e tests where appropriate

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[bentsherman]

Tests are failing due to Wave?

~ Test 'fusion-symlink.nf' run failed
   + '[' -z *** ']'
   + echo initial run
   initial run
   + /home/runner/work/nextflow/nextflow/nextflow -q run ../../fusion-symlink.nf -c .config
   ERROR ~ Error executing process > 'CREATE'
   
   Caused by:
     Process `CREATE` terminated with an error exit status (125)
   
   
   Command executed:
   
     echo HELLO > data.txt
   
   Command exit status:
     125
   
   Command output:
     (empty)
   
   Command error:
     Unable to find image 'wave.seqera.io/wt/e7b9795c2b58/nextflow/tests:latest' locally
     latest: Pulling from wt/e7b9795c2b58/nextflow/tests
     a3ed95caeb02: Already exists
     1b3e7701db96: Already exists
     a3ed95caeb02: Already exists
     a3ed95caeb02: Already exists
     486f7ff2dd95: Already exists
     009b1e9adc43: Already exists
     5ca4cba2c0a3: Already exists
     2997c9ef2ef5: Already exists
     a3ed95caeb02: Already exists
     a3ed95caeb02: Already exists
     a3ed95caeb02: Already exists
     140836dbc286: Already exists
     eed831c78eec: Already exists
     ac6d42ea81bb: Already exists
     f9510fa3a08f: Already exists
     3dca4ae9f36c: Already exists
     a3ed95caeb02: Already exists
     ceb5650fa213: Pulling fs layer
     dd97694ce7a4: Pulling fs layer
     ceb5650fa213: Verifying Checksum
     ceb5650fa213: Download complete
     ceb5650fa213: Pull complete
     dd97694ce7a4: Verifying Checksum
     docker: filesystem layer verification failed for digest sha256:dd97694ce7a42d826212b59d13df70a643c0192533becd68d9e867f88297c996.
     See 'docker run --help'.
   
   Work dir:
     s3://nextflow-ci/work/89/87e1d9b4c45dedc5006c8f69003[733](https://github.com/nextflow-io/nextflow/actions/runs/12281095140/job/34269672962?pr=5502#step:5:734)
   
   Container:
     wave.seqera.io/wt/e7b9795c2b58/nextflow/tests:latest

[pditommaso]

I think it's a Fusion issue @alberto-miranda

[christopher-hakkaart]

One very minor suggestions. Otherwise the docs look great.