Refactor filesystem abstraction to and use it in production

[Geod24]

Extracted from #2941

The filesystem abstraction needs to be known to production to avoid
too much code duplication. So far we have used functions in
`PackageManager` that the `TestPackageManager overrides.

With this change, we can remove them, and instead just pass an interface.
On the long run, we should be able to do dependency injection simply
by passing a different object (or overriding) the `Dub` class.

An initial attempt made `FSEntry` inherit from the `Filesystem` interface,
however that attempt was doomed as it conflates two different abstractions:
`FSEntry` is a "node" in the filesystem, which we want to act on in one
of multiple ways: move to another node, or take an action. On the other hand,
`Filesystem` is a more generic interface and takes a path as most of its
function's argument. A `path` and an `FSEntry` have a lot of overlap
(they are a reference to a node in a tree) and the resulting interface
would have been very clunky.

[github-actions]

✅ PR OK, no changes in deprecations or warnings

Total deprecations: 0

Total warnings: 0

Build statistics:

 statistics (-before, +after)
-executable size=5263712 bin/dub
-rough build time=60s
+executable size=5289208 bin/dub
+rough build time=61s

Full build output

DUB version 1.37.0, built on May 11 2024
LDC - the LLVM D compiler (1.38.0):
  based on DMD v2.108.1 and LLVM 18.1.5
  built with LDC - the LLVM D compiler (1.38.0)
  Default target: x86_64-unknown-linux-gnu
  Host CPU: znver3
  http://dlang.org - http://wiki.dlang.org/LDC


  Registered Targets:
    aarch64     - AArch64 (little endian)
    aarch64_32  - AArch64 (little endian ILP32)
    aarch64_be  - AArch64 (big endian)
    amdgcn      - AMD GCN GPUs
    arm         - ARM
    arm64       - ARM64 (little endian)
    arm64_32    - ARM64 (little endian ILP32)
    armeb       - ARM (big endian)
    avr         - Atmel AVR Microcontroller
    bpf         - BPF (host endian)
    bpfeb       - BPF (big endian)
    bpfel       - BPF (little endian)
    hexagon     - Hexagon
    lanai       - Lanai
    loongarch32 - 32-bit LoongArch
    loongarch64 - 64-bit LoongArch
    mips        - MIPS (32-bit big endian)
    mips64      - MIPS (64-bit big endian)
    mips64el    - MIPS (64-bit little endian)
    mipsel      - MIPS (32-bit little endian)
    msp430      - MSP430 [experimental]
    nvptx       - NVIDIA PTX 32-bit
    nvptx64     - NVIDIA PTX 64-bit
    ppc32       - PowerPC 32
    ppc32le     - PowerPC 32 LE
    ppc64       - PowerPC 64
    ppc64le     - PowerPC 64 LE
    r600        - AMD GPUs HD2XXX-HD6XXX
    riscv32     - 32-bit RISC-V
    riscv64     - 64-bit RISC-V
    sparc       - Sparc
    sparcel     - Sparc LE
    sparcv9     - Sparc V9
    spirv       - SPIR-V Logical
    spirv32     - SPIR-V 32-bit
    spirv64     - SPIR-V 64-bit
    systemz     - SystemZ
    thumb       - Thumb
    thumbeb     - Thumb (big endian)
    ve          - VE
    wasm32      - WebAssembly 32-bit
    wasm64      - WebAssembly 64-bit
    x86         - 32-bit X86: Pentium-Pro and above
    x86-64      - 64-bit X86: EM64T and AMD64
    xcore       - XCore
   Upgrading project in /home/runner/work/dub/dub/
    Starting Performing "release" build using /opt/hostedtoolcache/dc/ldc2-1.38.0/x64/ldc2-1.38.0-linux-x86_64/bin/ldc2 for x86_64.
    Building dub 1.38.1-rc.1+commit.65.g8dfac23b: building configuration [application]
     Linking dub
STAT:statistics (-before, +after)
STAT:executable size=5289208 bin/dub
STAT:rough build time=61s